There are a number of incompatibilities caused by outright different function names ("tfeestimate" in Matlab vs "tfe" in Octave for transfer function computations for example) or the order of input arguments in functions. Also, there are several functions in Matlab that don't exist yet in Octave.
Interesting. I find with small utilities that I download, Octave runs matlab fine. With bigger things (optimization packages in my case) you do hit incompatibilities. I guess I don't use the latter that much.