It happens on American with their new automated booking system.
The AURA system will clear standbys and take your seat if your connecting flight is a little late - even if you run to the gate and make it before the gate closes.
Last month American Airlines fully rolled out a new tool called AURA, the “AUtomated ReAccommodation” tool to rebook passengers when their flights are cancelled or delayed. But this tool does so predictively. And it's causing seats to be given away from passengers that make their flight.