Sure they did, you only get 90 days free telephone support. Only get more if you buy AppleCare.
IMO I always thought this was only if you required them to do moderate troubleshooting over the phone or something. I've called Apple up a couple of times regarding basic technical enquiries even though I'm out of support and they've always helped me out free of charge. Did you ask them to remotely access your computer and check on it or something, because that might have explained why they billed you.
Anyway take it back to the shop to get them to check it out again. Next time some "genius" tells you that they've ran the tests and it's fine, ask him back this question: "If it's fine as you claim it to be, then could you kindly explain to me why am I experiencing all these <list of problems that you've had> issues? Because there's obviously something wrong with it as it was beeping on me when I booted it up." Of course, start by asking them in a friendly, polite manner so they will be more willing to help you and don't be a jerk to them unless they're start being a douchebag first by giving you stupid answers telling you there's nothing wrong.
If they're going to insist that the tests show that nothing is wrong, then by all means go ahead and tell them to look at your record of all your Apple visits and how it's always the harddrive. Ask them if they honestly think that you have so much free time to constantly pay them a visit every few months, and ask them if they think you find it fun. Tell them that there IS something wrong with it otherwise you wouldn't be coming back so many times. If they still refuse to take a through check at it, then kindly request to them that you wish to speak to their manager.
Once they agree to take a look at it, then request from them if it's possible for them to get your notebook changed (or at the very least get the logic board swapped). If they tell you something like, "No, sorry we can't do that. We can only change the HDD for you.", then ask them if they know what the issue is. They'll likely say that they have no idea. Tell them that since they don't have any idea, what makes them think that changing the HDD again would solve the problem, as you've already had it changed many times and it is NOT fixing the problem, and they'll likely just be wasting their time and your time if they only swap the HDD again.
Also if possible, try to see if you can call up Apple again and ask them if they could at least make a case for you or something. Also ask them if they can help you request for a new laptop replacement as you've already had so many problems in 10 months. It'll certainly help facilitate things when you bring down your Mac to the genius bar again when you have a case ID from Apple Support. I had a problem once where I had an issue with my LCD, brought it down to the bar and they said they'll replace it. However I didn't have time then, and months later when I brought it down again the issue had disappeared and I was told they couldn't replace it any more. Called Apple up, explained to them and sent them pictures. Brought it down to the bar again and gave them my case ID and they took it in this time without questions.
Lastly as I said, try to remain friendly and polite to the staff.
At the end of it all I think you can try to call Apple back and ask them if they can waive off the $50 charge too. Explain to them that it was due to a fault in the computer that caused you to call up, and you don't feel it's fair that you have to pay the cost for it.
PS: Don't get an SSD just because of this. If you had 4 HDD failures within 10 months then there's an extremely high chance of there being something within your computer causing it to fail, and it's possible you may end up killing another SSD too.