This is a reasonable thing for the contributor to include in their modification to your project. It is normal for modifications to an open source project to include copyright notices of (up to) everyone who ever introduced copyrightable changes into the work, because each contributor holds copyright to their contributions. You say the copyright notice "isn't needed" which is largely true -- copyright notices don't serve a significant legal function anymore -- but neither is it incorrect or a hindrance to your project's license.
It has no impact on the usability of your project under the MIT license, as long as the contributor is clear their intent is to also license their contribution under the same license. This is a normal expectation called "inbound=outbound". For an MIT-licensed project especially, it doesn't hurt to be crystal clear on this point. For Apache licensed projects, this is actually encoded in the license text (exceptions to the rule must be labeled "not a contribution"), and for GPL projects, any modification that isn't GPL'd is copyright infringement, but for MIT projects, a fork could reasonably introduce proprietary code without a legal issue.
In the absence of any intent to license under non-MIT terms (and especially in the face of a positive intent to use MIT terms) you may freely incorporate the changes from the contributor's fork. You are free to reject the PR, or free to accept under the terms they offer it (probably the same license your project already has), but you are not free to remove the copyright notice present on their changes, as this is one of the few requirements of the MIT license.