There's a limit for as many entities a map can hold. Once reached you get these invisible models or other scripting related entities simply not firing as they too are in a sort of invisible state aka not properly compiled along with the map.
Having 250 models in a map is way way to much. Why do you think did most mappers while we're talking about a forest using impassible routes, diverted with rivers and impassible hills? All that while the actual walk space is almost corridor thick? Just because of that very same named entity limit.
Best you use forest background textures and create a wall on the outer map edges with some isolated trees before and behind that forest texture wall in order to not make it to obvious for the player.
HL engine limits for ALL entitys - 2048
HL in-game temporary entity engine limit (part of the 2048?). Used for breakables, sparks, gibs, ect. 500
data memory limit for entitys ~0.5M
MAX_MAP_ENTITIES Compiling tools limit for ALL editor placed entitys in a level, incuding brush, models, sprites & point entitys like lights (mod limits may vary a bit lower) 2048
MAX_ENGINE_ENTITIES (light, light_spot and light_environment entities that have either a targetname or a style attached to them (ie. all switchable lighting in the map). 1024
compiling tools sub-limit of brush based entitys (part of the 2048) 400
possible model & sprite entitys sub-limit (part of the 2048?) 400
specialty entity limits
By now it's a little more if you use these compilers
https://forums.svencoop.com/showthread.php/42174-Vluzacn-s-ZHLT-v34-UpdateBut the limitation is still present.
There's also the possibility that some of the models are stuck half inside the map or that there are micro leaks nearby or created by the models themselves which could also ruin their appearance and the compile log won't display it then. I had such a case once and redid the specific section in order to fix it.