The drain hole are not too small, nor does the oil need room for expansion. If either were the case, the oil level would have shown 1qt low after every oil change since 1999. As honestly as I can, Jiffy Lube is just making excuses for their incompetence of not adding the correct amount of oil.
The only legitimate reason for it showing low if not actually low would be if either the tip of the oil dipstick was broken or there was something blocking the dipstick in the dipstick tube from seating all the way. Since neither is mentioned by you, I assume it is not broken and it seats all the way in the dipstick tube.
Add 1 qt of oil to bring it up to correct level and I would suggest finding another shop to do the oil changes in the future
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