Missing Files after Yosemite update

I cleaned out my computer & backed up on Time Machine plus two external HDDs then downloaded Yosemite
75% of the older files are now missing & that applies to Time Machine & the HDDs it is as if I never backed up ever
Mail has become erratic it was never very good on maverick but now incoming messages go where they want some go to the account some to archive some to trash some to junk totally erratic
If any other companies produced goods like Apple & Microsoft that continually go wrong they would be out of business very quickly how are they allowed to get away with it it is the biggest con this century
I know this isn't the place to rant & throw me off if you don't like it but imagine if you had a car that was as unstable as most computers

Not defending Apple but something else is going on here. If you were backing up using Time Machine and the backup completed successfully the files should be there. If Yosemite had a habit of eating Time Machine backups we'd have heard a lot more about it by now.

As far as mail files being moved to erratic places again there must be something odd here. I've been using Yosemite since the first public beta and haven't experienced these problems. We need a bit more information to solve this one.

1. Does this happen every time you receive mail?
2. Does it happen to the mail coming into only one or two accounts or all of them?
3. Do you have any rules set up for handling mail?

Thanks Slydude for replying
Yes this happens every-time I receive mail & on more then one account plus I have no rules set
Something I have just remembered I noticed I had gained a lot of disc space after I had downloaded Yosemite which may be an indicator to the missing files

Thanks again for giving me your time