Thanks for the bug report.
Firstly please open a separate bug about the clicking issue (although it
sounds related to bug 2063831). We need each bug report to only describe
one problem.
For the window borders issue please try:
1. Deleting all local extensions:
cd ~/.local/share/gnome-shell/
** Summary changed:
- No windows margins, problems with detecting windows on clicks
+ Window borders and shadows missing from GTK dialogs
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