Once you cut into wood - you expose 'end grain', if you think about wood as a cellular structure similar to a bunch of drinking straws - the end grain is the open end.
Cutting into and exposing the open cells allows the stain or finish to leech into the open cells - flooding them -they will also suck the stuff in due to capilliary action - this results in an uneven darker finish. If you have ever tried staining a stock - you will notice the end grain finishes darker - only way to prevent this is to apply an inert sealer coat first!
Hope that explains it!
ASM