In your case because you had not been to the gym for a long time, your sore shoulder muscles may have nothing to do with the
cipro and it may just be coincidental.
When you have not exercised for a long time and then start to exercise again, everything feels sore and tender.
Had you been exercising at the gym non stop and got the muscle soreness when taking the cipro, then yes, I would have suspected that may have been a side effect from the cipro.