I'm working on a college design project and need to know;
what are some problems, challenges or just general annoyances you've had learning or playing music? Any contribute is appreciated.
Something general for me is not knowing how to efficiently spread my practice schedule.

In practice/theory for me now I try to use different scale for each chord in the progression and it's kinda hard at times, some times I "lose" the backing track and have no idea what chords plays at the moment, so I guess aural training is crucial and also probably one of the hardest things for me, yeah. AURAL TRAINING

I think also keeping track of what you learn n practice and the progress of what you're working on is very important, I want to learn new solo, work on it for few hours and then I move to another solo and never finish a single solo... being organized helps
For me it was basic music theory, like learning the names of the strings and the notes on them. After that is was learning your basic chords and learning how to finger them properly as well as changing through them. Then it was the vocabulary like octives, flatted 5th and arpeggio's. Its a never ending process but a fun one as well.
Sometimes I find it hard that I have to get through four hours of practice between 3 styles rhythm, lead, and finger style. It can get really irritating at times to remain discipline, but if I didn't I would probably suck.

Focus, practise and going forward. Also using a metronome to keep time as it works wonder for my skills.

That kind of sums up 20 odd years of experience being a guitar player.
For me, the biggest challenge was reading music fluently. That put me off music theory for a very long time (this was before the tons of stuff was available on the Internet). I'm stilll an attrocious sight reader, but I understand theory now, from other methods.