I have had this happen to me and it's a real pain. Transmission has probably been shut down abruptly and left a corrupt file or directory on your filesystem. You may find it affects other parts of the phone. In my case I recall it left me unable to mount the internal storage as USB mass storage on my PC.
I managed to fix mine by going into the directory structure via the terminal and manually deleting the offending files from the Download directory, but it took a long time and a number of reboots.

Sorry I can't offer more help. I would strongly recommend that anyone using Transmission save the torrents down to your SD card rather than internal memory.