How did Calvin end up there without being seen?

Hugh has some strange, inexplicable (read : stupid) bond with Calvin from the beginning. He's the only one calling it Calvin, like it's a person. He feels that the world's stem cell research (and possibly healing paraplegic folks like himself) would take a leap ahead because of Calvin.

Calvin has other plans. It wants to consume them. After Calvin enters back from those thrusters .. it makes its way to the group.

ref : Life (2017) Explained

Let's take a minute and see what Hugh is up to here. Hugh has some crazy affinity with Calvin. He sees Calvin approach while the others are taping up the place. He doesn’t say anything. He actually allows Calvin to latch on to his leg. He then goes on to talk about how the nature of life is through destruction. How Calvin doesn’t hate them but has to kill them for its own survival. He then touches his leg and then begins to lose consciousness. Then he says “I’m sorry”. Hugh's helping Calvin here. He's lost it and the crew doesn't realize this.

(There is a pic of Hugh's hand on his leg too) So Hugh seems to have allowed this to happen.

Regarding Calvin making his way into Hugh's pants:

As some have already pointed out; Hugh was weak and injured ? - he also has some weird affinity with the organism. So yes, it may have been intentional but also remember Hugh hadn't got the use of his legs. Calvin has repeatedly demonstrated a frighteningly high level of intelligence at this point. Messing with Cat's coolant system in her suit. Sho says (during that scene) that "Calvin knows exactly what he's doing!"

So as well as Hugh having no sensation in his legs I'm pretty sure Calvin has the gumption to figure out that crawling UP the leg of the suit is probably the desirable method here.

I mean... he was clever enough to push his escape pod towards earth via mr gyllenhall

After Calvin reentered through the thrusters when no one was looking, Calvin latched onto Hughes's leg. Hughes did not know he was latching onto his leg but the movie had a good misdirection about if he did or not. We all know that Huges is a paraplegic and most vulnerable also because he was the closest to the compartment opening.

There was a scene shortly before, from Calvin's point of view, where he (it?) is tracking Hugh. Hugh is standing behind the others, who are looking the other way. Hugh looks up into Calvin's POV, the music surges, and then the scene cuts to a shot of David and Miranda, without Hugh in view. Shortly thereafter, he comes into view and then collapses. That's when they finally discover Calvin in Hugh's pants.

The implication being that Calvin slipped into Hugh's suit at that point.

As far as why Hugh didn't mention the monster in his pants, it was likely that he was too stunned/drained/sick to mention it. Or he could have just decided not to (since he felt fatherly towards it).

Clearly Calvin enters Hughs' pants the moment you see everything from Calvins' POV. Whether or not Hugh realizes it at that moment or just a little later on ('cause he sure knows when he's dying) is up to anyones' speculation I guess...