Considering what we've seen and what he knows about BOB there's no reason for him to consider that BOB is a doctor, so why does he ask?

I have a theory and it has to do with the extended ending of the Pilot, where Mike says literally that BOB "sometimes work among the infirmed, the injured of the species", so maybe that's where he got it... If the writers of ep.4 still considered the extended ending to be Coop's dream like in ep.3 (with Lucy, Harry, BOB being shot and Hawk doing sketches) this could be the answer and why Coop thinks that...

Any thoughts?

I don't recall that. I'll have to research. I thought Cooper just asked if he knows a BOB and replies "Bob Lydecker's just about the best veterinarian in these parts."   Hence, the officials look up the office.

It still doesn't contradict working among the sick.

EDIT: Well, according to the script, he does ask if BOB's a doctor.  There are other references to the Euro pilot in the series, too.  It shouldn't really faze anyone who hasn't seen it first. Just accept Cooper's intuitive genius, I guess.  

That's what I thought at first: Coop's incredible intuition. But that would be a too easy explanation... Later in the ep. Coop shows that intuition when he asks Andy to buy twine and knows it's going to be Finley Fine Twine, the same one found in Laura's upper arms, but though it's amazing how he knew that he's just putting pieces together: the OAM's best friend is named Bob, is a doctor, has his clinic next to a convenience store,... He also knew that the bird who attacked Laura was attended at the clinic...

But he asks if BOB is a doctor out of nowhere, without anything to back up his intuition (if we exclude the Euro ending)... That's odd...

 Hey, it's my first post, hurrah!

 Nefud, love your TARDIS icon!

Let me advance this theory... Have you ever thought that maybe those elements are just metaphors?

"We live above convenience..."  "Work amongst the injured..."

I could go on with examples from both the movie and the series, but I'm sick so I stop here.

"Did they scoff the whole damn Smörgåsbord?" (Audrey) 

"Gimme a donut!" (Coop)

The "infirmed of the species" comment is part of it...

The reason Coop asks if BOB is a doctor is that in his dream Gerard called him in the middle of the night and asked to meet at the HOSPITAL.  Coop says "I saw you, you were in an elevator here..." (something like that) and Gerard says that he was there looking for BOB because he sometimes works... etc.

In ep 3 when he is retelling the dream, he doesn't mention that it was a hospital to Lucy and Harry.

In ep 4, he's trying to piece all the clues together.  We haven't been given all of them unless we've seen the extended pilot, however.