Won't say that git has never messed up ... experienced that one time, but that was due to the repo being down an resolved using an alt git repo.
git pull will do that ... pull some files and modify some and even delete some ... but 'miss'? Rare, I'd say.
Glad that you had the presence of mind to try an alt way of getting core code, but now that you have used wget, you've lost ability to easily acquire updates/upgrades. :|
Could you supply some info on failure of git to work?
'SoS', Ken