Hi @droslj
Apologies for the delay. I was able to reproduce the problems with even with our test data.
When working at UseGalaxy.org, the output option is PDF (only).
A cross-test at UseGalaxy.eu produced correct graphics for PDF, PNG, SVG, and JPEG.
The tool has a bunch of usage disclaimers in the help section. Still, I think this is worth tracking and so created a ticket Fix-up graphics to support more output types for snpfreqplot at ORG · Issue #628 · galaxyproject/usegalaxy-tools · GitHub if interested or want to follow it. When that closes out, then you can try at UseGalaxy.org again.
For now, please try at UseGalaxy.eu if you haven’t already.
Thanks for reporting the issue!