The physical presence count uses the application date, not the 5 year anniversary nor the interview date. Trips abroad or time staying in the US after the application date don't affect the physical presence count. This has been confirmed in court.
You need at least 913 days within the US in the past 5 years before applying. You said you were about a month short of having 900 days outside the US ... so that's about 870 days outside the US. However, because you applied about 3 months before the 5 year anniversary, that means you applied when were a permanent resident for about 1736 days (5 times 365 = 1825, plus 1 day for the 2008 leap year = 1826, minus 90 days = 1736).
870 days outside the US would mean 1736-870=866 days inside the US as of the application date, which means you failed to meet the physical presence test.
In addition, if you applied 3 calendar months before the 5 year anniversary, and those months are such that you applied more than 90 days before the 5 year anniversary, you would have applied too early, because the regulation allows a 90-day headstart, not 3 months. Sometimes 3 months is 91 days or 92 days. However, since they're supposed to look at the date they received it and not the postmark date, you'll probably be OK if you sent it exactly on the 3-month mark, since the day or days in transit probably would have made it cross the 90-day mark by the time they got it.