Certain stains have the characteristic ability to darken the wood as they cure and once this happens, any further application without completing the board will result in lap marks.( -------==-------- ) Others don't have the ability to absorb themselves once the product has begun to set up.
Lap marks are a nature of the beast according to product being applied.
Getting rid of lap marks using mineral spirits, thinners, Xylene, goof off etc. are just some of the ideas you may get here, but be careful, what you do may also affect the finish and longevity of it as well.
My suggestion is to follow the labeled directions to remove them if prescribed there, otherwise, you may need to virtually strip the affected areas and recoat with a blending technique.
Once you take care of that issue try this to avoid the problem in the future; Once you start a board, finish the board. Never do a series of 'cutting in' (working the edges of a large area first then coating the rest of the section). Keep mineral spirits on hand to help with any over applications and over-lapping before the product sets up. Put any rags used in the clean up process in a bucket of water to avoid spontaneous combustion.
Rod!~