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Missing "green".
Did you download this already?
http://arcarc.xmission.com/PDF_Arcade_Manuals_and_Schematics/Aliens_Schematics_(Konami).pdf
By the looks of it, part of the video output chain that is shared by both the tilemap and sprite layers is buggered.
I'd start at the array of LS153s (I13/H13/G12/G13; schematic page 3/4) and work towards the palette RAM and DACs.