Git can handle the situation where applying patches and pulling the same changes have been mixed in one repository. Even though the commit in the receiving repository ultimately differs from the commit in the original repository from which the patch was made, Git can use its ability to compare and match content to sort matters out.
Later, for example, subsequent diffs will show no content changes. The log message and author information will also be the same as they were conveyed in the patch mail, but information such as the date and SHA1 will be different.
Directly fetching and merging a branch with a complex history will yield a different history in the receiving repository than the history that results from a patching sequence. Remember, one of the effects of creating a patch sequence on a complex branch is to topologically sort the graph into a linearized history. Hence, applying it to another repository yields a linearized history that wasn’t in the original.
Depending on your development style and your ultimate intent, having the original development history linearized within the receiving repository may or may not be a problem for you and your project. At the very least, you have lost the complete branch history that led to the patch sequence. At best, you simply don’t care how you arrived at the patch sequence.