So I started my Phd last year, in the field of high power lasers.
The big problem is when my supervisor expect me to arrive in the office. During my first year no restriction was put on starting and ending times, so I'd try to come in at around 9am and leave 5pm, but I have a long running health problem which means sometimes I come in late, but I figured it was fine as long as I work later into the day.
Now at the start of my second year my supervisor has been enforce a 9:30am starting time. This is totally fair but again there are days where I struggle to be in at this time. After being late a few time I was called to my supervisor office. He is rarely around so he told by one of the RAs I share an office with. I told him about my health problems, that I've been in and out of hospital trying to solve it. He told me "I don't think that's a good enough reason to not being in the office at 9:30". He thinks that's the group is not making enough progress and that PhDs being late is the reasons behind. Since then I have been trying to make it in. I know I was very lucky to have the flexibility at the start which I wouldn't normal have in a normal job.
But as winter rolled around my joints have gotten worse so I've been late again, usually 10am. Since my supervisor is never around the RAs having being reminding me a lot. After being late today one RAs told myself and another PhD "I am upset about you both being late, we have tried the soft way, now we are trying the hard way." He did not explain to us what the hard way was.
I am not to sure how to proceed with this, I am trying to get my health in order but I find the pressure and threats stressful.

I have to say that in my opinion, unless there are safety issues, it is not reasonable for a supervisor to be dictating what specific hours a fully grown adult student should be working in 2019. I asked questions about this during my interview and it was one of my red lines. I came and went as I pleased.

Not sure why you are talking to an RA. Those guys are not permanent employees are they? Either way, they are not responsible for your welfare and I would email your actual boss explaining your health concerns and also approach the university student services. You should consider reporting the threats you are receiving.

I usually work 10am- 6pm and my supervisor is fine with it, since she knows I stay that bit later. I don't agree with clock watching but if you turn up late you should make the appearance that you all stay late. PhDs have great flexibility but you are still expected to put in the hours and get results. If you can argue both of those points to your RAs they will shut up.

Though I am in the UK with guaranteed funding and my supervisor cant strip me of it.

This is bullshit. If your university in Europe, you should be firm about your health problem with supervisor and even report his behaviour. About this a**hole RA, be more firm and tell him you have a boss to talk to and it is not his business to decide for you what time to show up at office.
Now the scary part if you are in one the countries where oppression and forced labour are not uncommon, then talk to supervisor and tell him it is not possible to do this and you spend 8 or 9 hours nevertheless at work. Tell him about this bullying RA and get this thing clear and understood that you won't go everyday to work with fear.
Otherwise quitting is still an option. I do not see any good coming from this environment if things stayed the same.

eng77, I agree with you regarding the RA but I would probably find out from my supervisor what power he had allowed them to yield first. Personally, I would have had this ironed out during the interview and it would have been another of my red lines - I would only work directly for one supervisor and not a range of his minions. An RA talking to me like that would be told squarely to fuck off. The other problem the OP has is that they have joined a team. Again this isn't something I would ever agree to because it just becomes an invitation for others to control me. It's a difficult situation all round for the OP.

Your health condition might be classified as a disability (if it's long term and adversely affects your ability to do day to day activities) and if so you are entitled to reasonable adjustments, which could include a later start in the morning. You should talk to student services or the disability service if your university has one.

I don't understand why the RA is making such a fuss unless your late arrival affects the team's ability to get things done. It sounds as if they're just a crazy control freak.