Why did my application got denied in May 2014 based on breaking the continuous residency?

I have been a GC holder since 1995. I left the country in 2009 for 9 months and returned Dec 14th 2009 (breaking my continuous residence and starting the clock again). I made up time and applied for N-400 in February 2014 under the 4 year 1 day rule. My application got denied in May 2014 based on breaking the continuous residency. My question is why did this happen if I followed the 4 year 1 day rule? and my next questions is that on Dec 15, 2014 marks the 5 year mark since I broke the continuous stay, Can I apply 90 days before then or do I need to wait till that date? And will I run into any more issues since I waited 5 years since my time away from the United States?