Yes, I agree that maple is tricky to stain and it does come out blotchy. That's because it doesn't absorb stain well. It's more noticeable with darker stains. Regarding cutting the wood, that is challenging to do once it's installed. However, they may be able to add a wood saddle or t-molding (pending the height) to cover this area.
Regarding the bubbles that can usually be fixed w/ a screening an extra coat of poly. sometimes that happens due to air bubbles when the poly is mixed or from poor application.
I agree w/ the comment on it depends on the quality of who you hired. A reputable place usually avoids this and/or if it happens will come back and address it.
Debbie Gartner, aka The Flooring Girl
http://TheFlooringGirl.comWestchester County, NY