I had this happen to me several years ago at MCO, whatever time frame they were still having you show your BP and ID at the gate as well as at the security checkpoint. At the time our travel office (governent organization) could only issue paper tickets on Airtran, so I had to check in at the ticket counter. I presented my ID and paper ticket and after the agent handed me my BP I was on my way. Showed BP and ID to both the security checkpoint person and the GA at boarding time.

It wasn't until I was seated on the plane that another guy came up and said he had my seat number. Turned out we had the same last name, different first names. The other guy mentioned having trouble checking in as the agent showed he already was checked in. The FA was flumoxed after we explained the situation - she stared at the BP for a minute - asked us "so you're not related?" (Not sure how that would've mattered) I was a 25 year old white guy and the other pax was an African-American senior citizen...the other guy quipped "yeah we're brothers, can't you tell?" She just looked more confused but went off to get a GA and eventually came back with a new BP for me. Luckily it wasn't a full flight.

I recalled looking at my seat assignment on the BP but I guess hadn't noticed the name. But neither did anyone at the security checkpoint or gate, despite having looked at my ID and BP. I did learn my lesson and always double checked from then on.