This problem is about automatical import optimization turned on. For example, if we take class under version control, i see into it, and IDEA show me import problem, i press Alt+Enter and IDEA append import into import list, also automaticaly optimized imports on fly. After this i press Ctrl+Z, and idea do not understand that i need to undo Auto import, maybe this command replaced in stack by optimization process. And finaly i get "Undo Undo?" dialog.

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