As a general rule, most characters have something they're good at and something they struggle with. While too much of the former is the most obvious cause of Sueishness, too much of the latter can also be bad for a character. If your characters manage to succeed at difficult tasks despite lacking any sort of skill or aptitude, it make readers wonder why exactly they somehow manage it. You could end up running into deus ex machina territory, or even Anti-Sues.

I'd suggest just poking around the wiki and trying to find an agent that's a good example of what you're looking for.

Everyone. Sort of. A bit.

See, it's no fun at all to have agents who are super duper good at their jobs - that way Suvianism lies. Instead, think about the people they are, think about who they are, and how that would help or hinder them in the field.

I kind of took this approach when designing my first Agent, Wobbles the Clown. She's a clown. Clowns are large and loud and brightly coloured, at least kids' clowns are anyway. This is distinctly suboptimal for covert operations. But wait - we have disguise generators for that sort of thing! Hm. Make them not work. How? Say, didn't Harry Dresden have this thing where he made tech go boom by moving close to it? How would this inform someone's character? Would that be a disability? How would she work, what would she be doing, why is she here at all...

And so on from there.

Of course, her partner's more renowned around these parts anyway, but her disability is that she's an incorrigible git. So there's that. =]