People make mistakes, and I have witnessed several different cases myself. I once withdrew from a sportsbook and received only like 30% of what I requested while the correct amount was removed from my balance. After speaking with the support, they told me I got mistaken for some other player who received my withdrawal amount and they gave me his. It was cleared up later. In a different situation, I was credited with 0.15 BTC in a signature campaign when I should have gotten only 0.015 BTC. Someone forgot the zero. The point is, people make mistakes, just be honest about it. That's not what happened with your coins, just remember that it could.
When it comes to Ledger Live and their servers, I haven't seen many glitches. But I remember an instant when my total balance fell to 0 during synching and then went up to the normal state a few seconds later. Not a pleasant experience as you might imagine. There was another situation where LL displayed I had like $100.000 more in BTC than what I really did. That again happened while the app was syncing.