Every tiny little imperfection used to bother me on a new handbag. A few years ago, a SA/Manager told me cowhides aren't perfect, hence the little imperfections. She wasn't trying to convince me to buy a bag (after looking at 5 of them, trying to find the "perfect" one) - only explain why you'll always find some irregularities. I've quit being so picky since then - but do try the one I'm most comfortable with.
That said, your spots on the INSIDE of the bag wouldn't bother me. However, if they were on the outside front, I would exchange it. It's all in what you can live with.
Imperfections, yes. Flaws - like messed up edge coating, flawed stitching, irregular dye marks etc - No, I exchange. Hope that makes sense!
I should add, I'm currently dealing with a "flaw" on a new 1941 glove-tanned duffle. It's the last Tabac/Carmine in existence. It has a loose thread, in the contrasting red-orange color, on the leather tab you pull the strap through. A stress point. My SA has tried daily to see if there are any returns. At this point, we're going to send the bag for repair. If the repair isn't acceptable, I can return the bag. Ordinarily, I'd return the bag... I don't want issues with the stitching coming out after a few months use. But I really want this bag.....