turn off kevlarman's stupid cg_projectileNudge option?
FYI I did as you asked and just now I played a game where the exact same thing happened (it was even on the same spot of atcs), only this time it was against a tyrant. Clearly this didn't solve the problem.
now that one looked more clear, as the tyrant was mostly in the line of fire.
the game logic works by "telemoving" players, one at a time, when move packets arrive at the server. by telemoving, i mean that when a player's position is to be updated, the player's bounding box is moved, and during this, the box is blocked by the world, movers, buildables, and other players, but the box does not touch trigger areas, buildable attack ranges, and missiles; at each server frame, missiles are moved forward, but in this case, they touch players (potentially causing a hit); also at each server frame, players are searched for in trigger areas and buildable attack ranges. due to this, it is generally possible for players to telemove through tesla generator and acid tube attack ranges without being attacked, telemove through trigger areas without activating the triggers, and as can apparently be seen, telemove through missiles without being hit.
but these cases require some combination of a packet burst and a lucky timing, to which a low sv_fps server setting contributes. mostly, the default/minimal cl_maxpackets client settings protect against such cases.
i'm also currently suspecting that a wrong (out-of-date) origin is used when launching missiles.
there's a case in which lucifer cannon balls fly through the energy core (a shootable object) on the
Operation: Blackout map, which may also be related.
on a side note, the server appears to be running on a low sv_fps setting (ie., 20 instead of 125) or you have a low snaps setting (ie., 20 instead of 99999).