Reinforcements spawing as either part of the hostile faction or the neutral faction depends on the value of percentageOutsideUfo that is defined for each rank in the reinforcement wave. If you want them to be part of the alien side, make sure it's set as
percentageOutsideUfo: 0
Any other value will set them to the neutral (or civilian) faction.
OMG it is even mentioned in the wiki, but in
Deployment Data section, and I did not paid attention to it
percentageOutsideUfo
Percentage (0-100%) of aliens to spawn outside of the UFO (in UFO land/crash sites).
Since OXCE 7.14, it can affect more deployments than just UFO landing/crash sites, see: forcePercentageOutsideUfo
For reinforcements, this attribute is reused/misused to specify whether to spawn enemies (use value 0) or civilians (use any other value than 0).
Thanks a lot CrazedHarpooner

EDIT: it is now mentioned in the
Reinforcements Script section