Increased pain after starting physical therapy?

Hi everyone, I was looking for some insight from others that have experience in working out to improve the symptoms of their hypermobility.

I began seeing a physiotherapist last October and we have reached a point where she described me "medical training therapy", which requires me to hit the gym three times a week and do a full body workout.

The exercises she planned for me are the following: Back Extensions Crunches Hip Abduction and Adduction Leg Presses Incline Pulls and Presses for Arms and Shoulders

I've been doing these diligently and safely for the past month, getting advice from the gym staff and only slowly increasing resistance, as per my PT's advice.

But I have been noticing increased pain in my tendons (especially knees and elbows) and lower back and shoulders.

To anyone with experience: Is this a "it gets worse before it gets better" situation and I'll adjust over time or are these the wrong exercises?

I don't think my PT is specialized in hypermobility, but I could not get second opinions til now, so I am starting to doubt the current therapy. Kindest thank yous to anyone that can add their two cents.