First off, both sentences are equally grammatical, make sense, and for all intents and purposes mean the same thing. The combination of "can" with "commonly" doesn't sit well with me, though. I'd prefer to either say it can be found, or is commonly found, but not a mix of the two. But that's really a question of style.
Secondly, your confusion stems from the fact that you think the verb "be" carries any meaning here. It does not. It is merely a helper verb that is used to form the passive voice. It does not imply or suggest the gel exists. It does not imply or suggest anything. It serves a purely grammatical function, not a semantic one.
Thirdly, in either sentence the repetition of "gel" is clumsy and grinding on the ears. You should replace the second occurrence with a pronoun (it). But this is once again a question of style and not grammar.
Lastly, the "with them" bit is superfluous (of course they carry it with themselves, who else would they carry it with?), and for that matter so is the "that carry it" bit (of course you can't find gel by killing a monster that doesn't carry it!). If you want to emphasize the fact that it's only some monsters and not others that carry gel with them, you could say just that: "some monsters", or "certain monsters".
So, in conclusion:
- Gel is commonly found by killing monsters.
- Gel can be found by killing certain monsters.