If it’s the exact problem, then you can fix it just by going through the theme tab and adjust the texture margins of the tres used. Maybe you can post some screenshots, and I’ll try to help.
The problem is that with the release of Godot versions, some parameters were renamed and now the engine does not parce them, I opened the ".tres" file using an editor and replaced "margin" with "textute_margin". However, there are still other parameters that need to be corrected, because in the end the theme still looks ugly.