The sequels went more heavily into the ‘cool’ greens than the first film, so it was a deliberate creative decision going forward (and seemingly, going back). http://www.dvdactive.com/editorial/articles/the-matrix-visual-comparison.html

The way I interpret the color shift from the first to the second film is that in the first one, the Matrix seems real from Neo’s point of view up until the end where he sees the green code running through the walls. The later films would then be heavily green because Neo sees that world as a computer simulation and his worldview has biased itself towards Zion and away from the Matrix.

Looking at the 35mm scan, there are many scenes that are still too yellow, and in particular the skin tones tend towards yellow even in the Nebuchadnezzar. Some scenes in the Matrix have a subtle green tint particularly in later scenes, but it’s far more subtle than even the DVD. I think this is accurate despite the uneven grading of this particular print, since I don’t see much evidence of the greenish-brown tint so prevalent in the DVD. “Deliberate Creative Decisions” were made for both the DVD and Blu-ray.