I wanted to put 50$ in bitcoin in the wallet from a certain website.
Did you try to use an online wallet (not recommended at all) or where you trying to
deposit BTC into a site (e.g. for buying stuff) ?
This makes a huge difference.
Usually, 'random' websites are not to be trusted.
The problem is that I dit it yesterday, and the transaction is called "complete" and over 55 confirmations now ( it keeps climbing ). I did the transaction yesterday but my wallet is still empty...
If the transaction is confirmed (which it is), the operator of the website DID receive your coins.
The fact that your 'wallet' (i guess you are referring to the credit on the specific site) is empty, means that either (1) there is an error handling the payment server-side (less probably) or (2) you have been scammed (more probable).
Without telling us what website it was (.onion site?), we unfortunately can't tell you whether it is a scam or not.
What should I do to get my 50$ back ?
Your only option is to contact the administrator / support of the website.
If they don't send it back to you voluntarily, there is no way of getting it back.