Unfortunately there is not a way to stop it.
If you have access to the design source file you can fix it. It’s a bit tricky and you’ll need separate pieces for each color, stacking them on top of each other but not assembled as a single piece.
I’m going to agree with this. While I’ve never separated a model for this purpose, I do design (simple) models in multi-color and separate/export each color into a different piece. I never have this issue with those models, but almost always have the issue with models that I color in Bambu/Orca.
What software are you using to design these? I could maybe (and I stress maybe, because I am far from an expert in anything) help you separate the models.
I’d be interested in seeing your technique. I’ve tried some bizarre things and haven’t had any luck.
I’ve tried to be really basic and just use BS/Orca and created a circle and a square - made one higher than the other and tried to slice and whether I leave them as separate pieces, or assemble them, I still get weird top layers.
This is all while maintaining the same color.
I’ve tried it with things I’ve designed in F360, as well as .stl’s I’ve pulled off various sites.
I’ll try my best to show what I mean.
Lets start with simple drawing. Just two circles.
Now, Lets extrude the outer circle up 20cm.
I also extruded the inner circle up 5cm, but forgot to screenshot that.
Under bodies, make two folders. One for each color. In this case, we’ll use red and blue.
Drag the body you just made into one of the folders.
Click the eye next to the folder to hide it.
Now, lets extrude the inner circle 20 cm to match the height of the outer circle.
And now 5cm off of the bottom to fit the 5cm we added with the first part.
Drag that new body into the other folder.
Exporting is simple. Click the eye on each body group to turn off visibility so that only one is visible. So, we’ll leave red on and turn off blue.
Now, export to your preferred format. I prefer step files.
Do the same for the other layer(s).
Now, open Bambu/Orca and drag both models in at the same time. You will get this message:
Click Yes.
Click on Objects in the left pane
Click on each object and select the color by clicking the number on your keyboard that corresponds with the color in your AMS, or right click each object, hover over Change Filament, and select the color.
Slice it up and preview. You will see that it will print that color as deep down as you made the model. No more weird bleed through of other colors.
I hope my explanation was easy to understand. If not, just let me know and I’ll try to clear things up.
If you want a colored piece on top of another (say a logo) it’s still a bit more tricky. You can follow the steps above and export as a step file, but you will need to split the parts to objects and they will all be laying on the bed. To avoid that you need to make your top piece contact the bed by creating an assembly with a part modifier on the bed (a single layer is enough) then move the top pieces to the desired height. The slicer will show a warning because he thinks the object is floating but your top layer will be clean.
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If I’m understanding you correctly, no. If you follow my steps and drag both the file into Bambu/Orca, it will keep the in the exact place that they were in F360. If you look at the last screenshot, you will see that they are in the correct position by default using my method. You don’t need to move anything. It imports each part as separate objects, but locks them in place where they are supposed to be. You can even move it around and resize it. It won’t mess up the placement of anything.
So maybe I don’t understand what your design look like. Both cylinder have the same height ?
I’m sure your method works but not sure we are talking about the same use case.
I’ll try to share a 3mf to show how I do it, if there is a simpler method I’m happy to learn!
Let me know what you’re trying to design. I have nothing going on today. So, I’d love to give it a shot with my method and send it to you.
Yes, please, share the 3mf. I would love to see what you’re doing. Maybe there’s something I can learn from you, as well, because I’m not going to even try to pretend I’m an expert.
Here is an example 3mf: https://file.io/BkKz7ltUhcv5
Just a cylinder with a cube on top. With the standard method you will have the cube appear on the top layer of the cylinder, here if you slice you can check the top layer of the cylinder is clean. The little cylinder (almost a dot) is here to prevent the cube from being pulled down to the build plate by the slicer so it can sit on top of the cylinder.
It says the file has been deleted. 
[Edit] I see why it was deleted. File.io deletes the file after one download, and someone else downloaded it before I had a chance.
It was me, it’s the first time I’m using this service so I checked there was nothing wrong with the file before sharing… Here is the reupload: https://file.io/SFoqALnorfh3
I got it, this time. Give me just a little while.
Sure, here is another link for the next curious: https://file.io/thg3jTSuWeMn. I’ll need to find a better way for sharing. Unfortunately I can’t share a 3mf in the forum directly or I can’t figure out how to do it.
I looked at it, and I think I already see the issue. You have the square just sitting on the circle. The trick is to have it go through the circle a few millimeters, at the very least.
Give me a few to make one in my version.
@fabien I sliced your file and I see the clean layer.
@ihaveathumb I think you might be troubleshooting a slightly different issue.
It’s not really a color changing thing as much as it is a clean top layer.
Using his file, this is how his layer 50 looks. Its clean and how we want it. Unfortunately it thinks there is an issue.
I just assembled both pieces into one and then made a height modifier and made it 100% infill for a couple layers above/below the transition and it now looks like this. It has an artifact of the feature above it.
I’ve had this same issue with files I’ve made, files I’ve modified in the slicer, files I’ve downloaded, etc.
Yes this only works if the slicer thinks it’s 2 separate objects. If you assemble them, you’ll get your top layer issue again because the slicer prints it as a single object so it prepares the bottom of the upper object. It’s the right thing to do from the slicer perspective: it reduces the use of filament.
You can safely ignore the warnings in my 3mf, they are unavoidable. The slicer is not smart enough to figure out one object sits on top of the other so it thinks it’s floating in the air. It also tells there is a collision because the footprint created by the assembly of the cube and the dot collides with the footprint of the cylinder. But you can check it does what you expect when you slice it.
@fabien Here are my versions of your design. I included the 3mf, step files, and f360 file.
@nate4635 Am I? What am I not understanding? No sarcasm, either. Genuinely asking.
Did you forget the files ?
Lol! Yes, I did. My bad!