It could be down to several reasons.
A probe doesn't need to carry targeting systems (at least, not always, they can easily be programmed to follow a pre-set course, which is impractical for most torpedo applications), nor does it need to carry a warhead. the removal of these systems may make room for a small warp drive. With the miniscule mass of a torpedo, I don't imagine that it would require a particularly powerful unit.
Also, probes aren't always built off the torpedo base. As such, a probe may be designed with the ability to incorporate a small warp engine. Also, given the tactical requirements for a torpedo, a warp drive may be impractical - any anti-torpedo defense could easily track a warp signature, for example.