Any error of the type Bus error (core dumped) or Segmentation fault (core dumped) is the result of an internal bug in the package. There is little you can do unless you want to debug the source code yourself.
The main source of crashes seems to be sequence file input. The package tries to be very clever and flexible. Probably too clever. It automatically determines what format a file appears to be in. If you give an HMM program a format it doesn't expect, or a file that doesn't quite conform to the specifications of a format, it may choke in some inelegant way. You should make sure your file conforms to the format specification, or try a different format.
In any case, any bug of this type should be fixed. If you encounter one, please email me the circumstances of the failure, any data files necessary to reproduce the failure, and the HMMER version you are using.