same problem occured with me also.... very upseting
serious clock problems on live chess

I had 58 seconds on my clock, my opponent had 3.7 seconds. I made my move, my opponents clock ran down to zero six times, each time remaining on zero for at least two seconds, after my opponent made his move his clock regained 4-5 seconds. this is disturbing, this glitch or cheating is ruining blitz chess, can I contact an administrator? ?

It's called getting disconnected. Sometimes you disconnect and the client side, for whatever reason, doesn't notice. So, it looks like you are connected but really, your opponent is on the other end getting upset that you haven't moved and left them waiting.
I just had something like this happen a couple of days ago, and lost a game on time when I was really ahead. Every time my opponent made a move, my timer went way down on time. I was totally crushing my opponent, but I lost on time because of some technical glitch I had no control over. This needs to get addressed seriously and resolved. For as long as comments have been made here on this very topic, I can't help thinking that the staff at chess.com don't really care much about doing anything to fix this problem, and it's very frustrating.

I just had something like this happen a couple of days ago, and lost a game on time when I was really ahead. Every time my opponent made a move, my timer went way down on time. I was totally crushing my opponent, but I lost on time because of some technical glitch I had no control over. This needs to get addressed seriously and resolved. For as long as comments have been made here on this very topic, I can't help thinking that the staff at chess.com don't really care much about doing anything to fix this problem, and it's very frustrating.
The part that can be fixed is how resilient the client is to disconnects and forcing a reconnect when it really isn't actually connected.
Your particular problem sounds more like lag, though it is also possible you were getting disconnected. The problem with lag, or intermittent network disconnects/resets, is that they may not be caused by something on chess.com's end or your client end (though, many times it really is something on the client end).
The only thing that can be worked on is how the client and server handles lag and compensating for it. That said, chess.com wouldn't be able to stay in business if they didn't care about such issues.
I always suggest taking a look over the following article (if you are on a PC). If you are on v2 of the site, disabling Flash when you are on will likely help some too.
https://support.chess.com/customer/en/portal/articles/1444918-my-internet-connection-is-fine---why-am-i-getting-disconnects-?b_id=12321
Another option is to try out v3 of the site instead.

Yes this clock bs is happening to me all the time but only when my opponent is loosing and it can say that i have disconnected can anyone recommend another chess site?
It's called getting disconnected. Sometimes you disconnect and the client side, for whatever reason, doesn't notice. So, it looks like you are connected but really, your opponent is on the other end getting upset that you haven't moved and left them waiting.
it happens after you disconnect.
The latest glitch I experienced was that the clock wouldn’t count down, like it was stuck, but the time would change after I moved and be stuck on the updated time.

It's a relief in some ways to see I'm not the only person facing unfair situations. I'm the one suffering from unfair things such as the clock problem and yet again I receive restricted b.s. note. "I must wait 5 minutes for the next game as a punishment for unfair play. Silliest thing I've ever seen.

an apology note to my person is in order. Please do something about it- dear admins and super admins....!

Also, I'm living in Iran now- I would be glad to pay membership fee but there's no credit card system. Please make some type of other transactions possible for people like me. You're losing in terms of millions as the result of this complication! I could help you in this regard. If you wish to have it resolved I have "solution"!

I have a feeling these things such as clock problem.... is due to free membership. It's not fair. I don't believe in such thing as free lunch; leave alone for ever, but how? It's not my fault

Also, I'm living in Iran now- I would be glad to pay membership fee but there's no credit card system. Please make some type of other transactions possible for people like me. You're losing in terms of millions as the result of this complication! I could help you in this regard. If you wish to have it resolved I have "solution"!
There are multiple methods of payment that do not require a credit card.
https://support.chess.com/customer/portal/articles/search?&q=payment
Though, with the site being US-based there may be other issues to contend with.

It's good this thread was started. Same thing happened to me today. Lost most of my games because of time. My opponents' time would freeze and regain the time lost as if he had an increment while I would lose more time than I should with every move! And this happened with every game all of which were played in the 5/0 format. I hope Chess.com fixes this immediately as it makes online gaming here unplayable.
I just lost another game when my opponents clock was at zero and mine shows over 3 minutes No time ran off his clock because it said zero and it would not let me do anything after about 3 minutes i lose on time and it wasn't my move what the hell someone needs to fix this