Yes, too high a grit and you burnish the surface, close up the pores and stain take-up can become very patchy. In general you really don't need to go higher than 180 grit before staining, though sometimes using a higher grit on just the end grain sections can stop those from taking up more stain and becoming darker than the rest of the body. The higher grits get used on the finish.

I haven't used it yet, but you can get a pre-stain conditioner than seems to get good results and evens out the stain absorption, reducing excessive end-grain take-up. No idea what people have used on here but a web search throws up a few hits.