What is meant by "alien" probe in a microarray?
It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent.


  The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that 
  is synthesized by in vitro transcription. The Alien RNA transcript is 
  nonhomologous to all known nucleic acid sequences currently in public 
  databases, as determined by BLAST comparisons against NIH sequence 
  databases. https://www.chem.agilent.com/Library/usermanuals/Public/300602.pdf


As any other external standard, you spike in the same amount of Alien RNA standard in your different reactions and then using the Alien probe you can normalize for extraction efficiencies etc. It works not only for microarrays, but also for qPCR, RNA-seq etc. 

If you didn't spike in any of it, I expect your probes giving very low signal that's probably why you thought about negative controls.