Traffic, lack of cycle lanes, getting a seat in a pub, people walking too slow, people carrying oversized umbrellas, public transport being too expensive, not enough healthy fast food places, puddles, roadworks, security, carpark prices, coffee prices
I agree that most are systemic problem and could be fixed with enough care and attention. But I would propose that a few are side effects of a healthy urban area, namely your last few: roadworks, security, carpark prices, and coffee prices.