Please open the file attached and watch the video.
Here is what happens, try to replicate it:

1. The document has a Layer 1 and it has a sublayer — Layer 2, which has one rectangle in it
2. If you select the Layer 1, the Make/Release Clipping mask button enables — click it
3. Notice that Ai underlines both Layer 2 AND <Rectangle>, as if they are both are clipping masks
4. If you click it again, everything is OK. But instead, select the Layer 2 and click the button after
5. See how Ai still shows Layer 2 underlined (bug #1)
6. Select a circle and see how the underline vanishes, and only <Rectangle> is now considered to be a mask
7. You can select circles and everything stays as it was, until you move one — then suddenly the canvas gets updated and all shapes get rendered as unclipped (bug #2). Sometimes it happens partially, and it seems to be unrelated to CPU/GPU view mode
8. Undo everything and clip again
9. Hide the rectangle and see how all circles get visibly unclipped — that is OK
10. Now toggle visibility…