While peppers are prolific cross-pollinators, you don't see the results of that in the original fruit. If you grow a habanero and a jalapeno next to each other, the fruit they produce will be exactly what you would expect from an ordinary jalapeno and an ordinary habanero. If you save the seeds, however, and grow the F1 hybrid it will be a mix of the two parents phenotypes. It won't look exactly like either parent, and will be some combination of the two in flavor.

If the original fruit you got from the jalapeno was different than you expected it could have been a hybrid itself, or it could have been growing conditions encouraged a spicier flavor.