It happened to me once and it was my error. YYZ-YEG, did electronic check-in and received e boarding pass the night before. Afternoon meeting did not go well, quickly checked seat availability for a later flight using my phone, in doing so, UNCHECKED myself and freed up my seat. Another PAX took the seat. When I showed up at airport and checked my luggage, the agent asked if I needed paper BP and I said no and proceeded with my e version not realizing that I had been assigned a different seat. Went through security, MLL and GA no issue to find seat taken on board. The FA quickly sorted it out with a call to the GA.