When going through a Nether portal, a player frequently spawns not where he should, but inside a wall close to the corresponding portal and starts to take suffocation damage (obviously). The game does that in both cases: when a player goes through a portal for the first time (the portal must be generated in the dimension player heads to) and when both portals (Nether and Overworld) are already generated.
Have fun fixing that :PP
And good luck <3