It can't be citric acid crystals, so it must be something else. I can't remember if there are any likely candidates among the citrates, but my guess is that something carried over from the developer is insoluble in acid solutions. Or something in your bottle...
In other words, you're not giving us enough information.
I think you're right but I still cannot trace back the problem.
Maybe it's some kind of bacterial growth, I've washed the bottle with quaternary ammonium salt and I've rinsed it well. Will see if it has solved the problem.