It's not something we are "upset" about, and considering the level of English you used throughout the rest of your post and response, I'm not sure "not a native" is a valid excuse.

I suspect if you aren't a native, the reason you say "my friends and me" is because it's a bad habit you've picked up from natives, like typing "gonna". I think anyone who can make a sentence such as,

"We cleaned up the procedure names manually, and matched the procedure related specialties to the hospital specialty ranking made by US News, and it gives much better perspective to the users"

is far beyond making English 101 mistakes confusing objects and subjects of sentences. Actually, in 15 years of on and off English teaching, I have run into very few non-natives who have that issue, since they had to actually study it. I find you to be somewhat unique.

In any case, there are plenty of natives who consistently say write and say this, so hopefully a few of them will take it to heart.