I think you're seeing the two of them grow apart. I feel Molly's biggest issue throughout the seasons has been around relationships and you see her really trying something different with Andrew and it seems that Issa isn't respecting that at all. On the flip, Issa's biggest issue has been around stability and finding her purpose and Molly doesn't appear to be respecting that. In my opinion, Molly has gone above and beyond for Issa, so I get why she didn't ask Andrew on Issa's behalf. It seems she's fed up and when she said "N!gg@ you always need a little favor", I felt that.
With that said, she was dead wrong for being pissed Issa went through Nathan. Andrew doesn't "belong" to Molly, where Nathan can't ask him a favor, not to mention Nathan knew him first.