Every time you put your car in the shop for maintenance there’s a chance something will not get put back together correctly. This phenomenon was first documented in WWII with a study conducted on the UK bomber force, and it still influences decisions on service intervals today. The gist is that the risk imposed by servicing the transmission fluid outweighs the risk of potentially contaminated fluid. This was confirmed via comprehensive testing conducted by the manufacturer. Some people–especially old school shade-tree types–find it difficult to trust the data.
Most owner’s manuals for newer cars with “lifetime” fluids include a requirement for inspection at periodic intervals. This generally requires checking the fluid level and sampling to determine fluid serviceability. If you find yourself continually fretting over the serviceability of your transmission fluid then change it for your peace of mind with the understanding you are introducing an element of risk that the procedure won’t be done correctly. If you can trust the data then take you car in for the periodic inspections and continue to drive it until told the fluid is no longer serviceable, at which point the risk of damage due to unserviceable fluid outweighs the risk of replacing it.
Did the shop fix your problem? Did someone from the shop explain why they did an oil change? If it’s part of the diagnostic and/or repair for the problem you reported then yes, they can charge you for it since you authorized the work.