[pk97]

exactly, it stands for "I have a question" :) It stems from the school/coaching system where you are encouraged to ask questions as you figure out say a problem set in dedicated "doubt clearing" sessions with your teachers/instructors. That carries over to the workplace where you are more likely to hear this phrase when someone has a question in a technical discussion or similar, from my observations.

[saurik]

This just seems like a tautology, as--from your description--it sounds like this is what I'd call a "q&a session", and so it may as well have become a "doubt clearing/solving session" because the teachers/instructors themselves also/already were taught that terminology... I'm wondering where it started, as, in English, the word "doubt" (especially as a noun) frankly almost never comes up, and if someone simply didn't learn it, they'd be fine?