Using "we" in mathematical reports
If you were writing for a journal, you would want to check the journal's style guide. If it doesn't cover that issue, then the next step would be to check previous publications and see what the norm is.

For an internal report with no applicable style guide, one should write for the intended reader/s. If your advisor is going to be the main reader for this document, then write it in the style that he requests.

To me, this change seems unnecessary, but it may help to consider this story from the development of the computer game Battlechess:


  The producers of the game were known to demand changes to the game, presumably to make their mark on the finished product. To this end, one animator added a small duck around the queen piece, but made sure that the sprite would be easily removable. Come review, the producers, predictably, okayed everything but asked for the duck to be removed.


In my experience, this is a very broad tendency among managers/advisors, and now that I'm a manager myself I understand the temptation to micro-manage. Even if a document is quite good enough as-is, if we don't suggest changes we don't feel like we're doing our job. 

It may be that your use of "we"s is the sacrificial "duck" shielding you from more annoying change requests.