Byproducts in Indigo Synthesis?
After looking further into indigo production, I came across a related structure called indirubin.

Indirubin:

Indigo:


Indirubin is a byproduct of indigo synthesis and has a reddish color. It may also be more soluble than indigo, and indirubin derivatives have some anticancer activity. If you trust this supplier, you can buy indirubin for pretty cheap to compare with your lab's indigo reactions.



I also found a study done on old native american dyes that studied indigo and indirubin in fabric fibers, among other dyes. They provide a UV-VIS spectrum of both compounds, with Ind = indigo and Inr = indirubin. We can see that indigo has an absorption peak in the red region, so blue is reflected. Indirubin has a peak at around 540 nm, which is yellow-green, allowing some blue and red to reflect, but probably more red than blue. This paper also references a 1910 paper** studying indirubin levels in commercially available indigo samples, but I can't find that article. They suggest that higher levels of indirubin are produced when more indoxyl is converted to isatin. If you can find this 1910 article, it may provide some insight into reducing isatin and indirubin levels.



** William Popplewell Bloxam and A. G. Perkin, J. Chem. Soc., Trans., 1910, 97, 1460-1475.