this seems to be the case, as happend to me with TSA at TUL. I had my liquids (all less than 3 oz) in a gallon sized ziplock bag. TSA caught it in xray and told me it had to be a quart sized bag.
me: Um, OK, but I only have this gallon size bag.
TSA: then these items can't fly
me: so you have no issue with the contents of the bag ?
TSA: no, the contents are fine
me: then what is the issue ?
TSA: you need a quart size bag
me: since the contents are safe and have already passed your screening, can I just put them in my computer bag and catch my flight ?
TSA: not without a quart size ziplock bag.
me: can I speak with a supervisor ?
TSA supv: you need a quart size bag
me: so the critical security issue here is not the liquids, but the ziplock bag ?
TSA: sir, we don't make the rules, if you don't like them, complain to your congressman
me: are you empowered in any way to apply common sense and actually see that there is no threat to aviation security here ?
TSA: no, we are not.
me: throw them in the trash, I have a flight to catch.

This is how it actually happened.