This sounds like it is almost certainly a broken GTK theme - either a bug in the theme, or a (GTK3) theme that is not compatible with your current version of GTK3 (GTK3 has stability problems - article).
First I would suggest testing it with the default GNOME Adwaita theme. If the problem goes away, then it likely the theme.
There were also some changes to panel sizing in 0.9.2. You can try the next branch (the upcoming 0.9.3), which includes a minor bugfix in this area. See the BUILD NEXT instructions in README (or the debian packager often offers git releases in his PPA).
If you are unable to resolve it with either of those, please open an issue on the tracker and include the output of 'spacefm --version', what GTK theme you're using, and reproducible steps. Thanks.
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