hmm, i never have those bursts without a reason, (i've got like 600k residents and 250k commerce in the city i am working on atm) about the money problems, dont build to much at the same time (services) and keep your eye on the cash flow
if something goes wrong, take a step back, the first thing you can do to get money is cutting health care, police or education a bit.
I do have 1 problem myself
i've got 250k commerce atm, but still no building bigger than 2000 jobs commerce, residents dont get above like 4k (only 1 tower has 10k pop)