To answer your question I need to watch this movie

Chilton carelessly left it behind. You can see Chilton accidentally leaving it on Lector's bed.

I thought it was on a table. How was Lector able to get it while still being in his straitjacket?

Could he have picked it up with his teeth? Or did he have that weird mask on already? I remember Chilton telling his staff to get Lecter ready to go... maybe that meant taking him out of the straitjacket, briefly.

I think he had the muzzle on then. He may have been able to get it with the wide openings on it with his teeth. The thing is, though, would they leave him alone without the straitjacket so that they couldn't see him. I would think someone as dangerous as him would be under watch 24/7.

I was coming here to ask this very question after watching the film again today. He was in the straightjacket when Dr. Chilton was talking to him. Yes, he left the pen, but there would be no way for Lecter to even get it, if he was bound in the straightjacket, with the muzzle over his mouth.

Another thing to question is how could Dr. Chilton even be that careless to leave anything in there with him? He was telling Agent Starling of all the precautions to take before she went to see him for the first time. So if he knows how dangerous Lecter is, how/why would he do that, unless it just wasn't reviewed by the director or continuity editor of the film?

Well, they had to have a way for Lector to escape and the pen is instrumental to his escape. I just wonder since Lector is in the straitjacket and muzzle how he was able to get the pen. I’m sure everyone there was watching him like a hawk. The mystery is how he was able to pull it off without being seen.