Currently im adding 2 droppers to my map.

They are both "func_instance" reflectocube droppers from the same vmf file,
and should be triggered at a different point in the puzzle.
The problem however is that when the map spawns, the left dropper is loaded with 2 cubes
and the right one with 0.

Also when the trigger activates, both droppers open their gates (with 2 cubes falling out of the wrong dropper)
I tried adding a fixupname to the instance, though it doesnt seem to have a impact.

How can i solve this?

This is the input going into the left dropper:

OnPowered
Dropper_Left
instance:@reflectocube_dropper;Trigger
<none>

OnPowered
Dropper_Left
instance:@reflectocube_dropper_autorespawn;Enable
<none>

And later in the puzzle another trigger does the right dropper:

OnTrigger
Dropper_Right
instance:@reflectocube_dropper;Trigger
<none>

OnTrigger
Dropper_Right
instance:@reflectocube_dropper_autorespawn;Enable
<none>

Also is it normal to have outputs for instances to be displayed with a disconnected icon, even though the text is from a dropdown menu?

Since your instances are identical, their sub-items' names are identical too. That's my bet why it doesn't work.

Kind of.

You need to use the "_multiple" version of the dropper. To my knowledge, there is not a "_multiple" version of the reflectocube instance. You can always copy the normal box dropper's "_multiple" version and modify it to use a reflectocube instead of a normal box.

Ill try that, should i only have to change the cube type of the cube floating at the top of the shaft?
or do i need to ajust some other paremeters?

Strange btw, that they dont have a "multiple" variant for the reflectocubes

Yeah there isn't a stock multiple reflectocube instance. I'm assuming because nowhere in the game do you ever get more than 1 (or rather, don't have more than 1 dropper for them). But it's easy enough to copy the normal_multiple instance and make the 1 small edit. Just be sure you change the names of the entities within the instance from "cube" to "reflectocube".

Ill try that, and ill try to make it into a usable instance at the same time

Though when looking through the list i found some strange droppertypes.
Do you maybe know what a "pendleton" dropper is?

No idea, I'd have to look and see what the entitites do.