You'll get this error if you f.ex. try to run code for a 68020 on a 68000.
The A2630 can supposedly be set to fall back to using the internal 68000 instead of its 68030, and I think 3.9 requires 68020, so it's one possible explanation.
If the 68030 is in use, then perhaps you've accidentally installed drivers or software that requires 68040 or 68060. In the worst case, the disc and software have simply been damaged.