Ordinarily I would simply say the email you received was ungrammatical in context, but this isn't the kind of error native speakers normally make, so let's consider it in more detail.
"I had done sth" (Past Perfect Simple) is usually used in contexts where we're already talking about some period in the past, but we need to indicate that this particular action took place even earlier.
OP hasn't provided the exact context of the preceding conversation, but possibly it was something along the lines of "I was expecting that report by now (or, yesterday), but I haven't received it". Note that OP himself can use past perfect simple to report this to us now, but it would have been incorrect to have used it while talking to his colleague).
Given such a context, it's at least possible (if slightly perverse) for the colleague to treat that time in the past (when OP realised he hadn't received the report) as being the time-frame of reference for the ongoing dialogue. In which case the past perfect simple is in fact appropriate.
So assuming the colleague is a careful, competent speaker, one might wish to consider why she chose to use a grammatically/logically justifiable, but slightly unusual, verb tense. It could, for example, indicate a certain level of exasperation or defensiveness. Placing the original sending even further back in the past may imply she thinks the prior history is now a matter of long-past events, and that they should "move on". Or that she acted correctly right at the beginning - so if anything's gone wrong since, it's not necessarily her fault.
TL;DR: In matters like this, OP should assume that native speakers probably know what they're doing. Hoping to catch them out in errors of grammar is a mug's game.