Three things come to mind:
Made a license called "GNU Free Documentation License" which isn't free. Claimed documentation
doesn't actually need to be free. Prohibited addition of plugin support for GCC for 10 years.
Of course if you're willing to conflate RMS-as-individual with FSF, there's many more. :)
Don't get me wrong, I do think FSF and RMS have been an overall positive by far, but they've also
done many remarkably stupid things.