I was a processor for a major bank. I did both prime and sub-prime loans. I can tell you that there are a couple of levels of underwriting that a loan undergoes. Every underwriter has things that are red flags for them, things that they are willing to accept, etc. The resolution of the issue may have been ok to the initial underwriter but then under final review the senior u/w may not like the condition.
Sometimes things are delayed intentionally to have funding occur at a certain time. I've been on both sides of this table - as processor and buyer. It is frustrating to say the least. Hopefully, things will get cleared up as quickly as possible and you can close on time.