Check that you don't have the deployment height set to 0 for this mission deployment.
I'm expecting it is something like this:
alienDeployments:
- type: STR_CUSTOM_TERROR_SITE_X
height: 0
I don't know if it is accurate, but the ruleset reference claims that the default value for height is 0. If so, then this means that you must specify a height for any non-vanilla missions, or else it will set it to 0.
So do this:
alienDeployments:
- type: STR_CUSTOM_TERROR_SITE_X
height: 3