Likely underestimating the time required...possibly quoting one type of service then doing another...possibly getting distracted by everything you find wrong and fixing/servicing it even when not part of the service quoted and/or requested/authorized.

if you are costing the shop money by doing 'free' services...ie...a customer brings in a bike for a basic tuneup, which takes less than one hour, and you spend 2+ hours on it because you service things that are not included possibly because the bike owner doesn't want to spend the money, etc. you are giving away service that is costing the shop money because you are being paid by the hour...

is the shop giving realistic service/repair estimates?
it depends on a lot of things but if i were the owner/manager and saw you performing hours of labor that was not 'quoted' or authorized by the bike owner i'd be having a conversation with you and perhaps if you didn't listen would be demoted to lesser jobs that i could watch you over and consider replacing you because i don't have time to watch over you and get my stuff done...

perhaps a 'list' of what is required for each service and you only do what is on the list and check off each item and when all checked off it is done...but who will create the list...as the owner/manager i'm too busy and shouldn't have to do this with an experienced/skilled mechanic...