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And further clarifications after reproducing the bug

When going to the actual question page, the flag info and actions appear in a separate frame at the bottom. If I click the close question button in that frame, the modal appears in that frame, but the frame is too small for the modal:

enter image description here

While the frame resizes and creates a scrollbar initially, moving the modal to the top results in the frame shrinking and top getting lost. I think the best solution would be to let the modal appear in the main frame, instead of the tiny frame at the bottom.