https://github.com/python/typing/issues/512 and https://github.com/python/typing/issues/511 are first issue (they are closely related to each other). This is not directly related to PEP 560, but changes in typing because of it will allow to fix them in a simple manner.

The second one is Union simplification (was discussed in few PRs on typing tracker). This is not really a bug, but something we should decide on before 3.7 final. It will be difficult to change it later. Again, with PEP 560 in place the corresponding refactoring for removal should be straightforward.

In addition, there is https://github.com/python/typing/issues/392, this is already almost fixed by the typing PR implementing PEP 560, but it doesn't work for dunder attributes (I think we should not relay only specific set of reserved names, rather than all dunders).