Recently I have experienced something new. I bottle condition all of my beer. I use corn sugar or DME depending on the beer/style. I have just drank the last of an ESB (WLP 002 English Ale) that was bottled 4-5 months ago and the last of a Wit (WLP 400 Belgian Wit) that was bottled 2.5 months ago. In both of them the yeast sediment has turned darker brown. No noticeable change in flavor, only cosmetic. Am I waiting too long or beginning to have OTHER (sanitation) issues?
I don’t think it’s a sanitization issue, I think the yeast is just not doing well. Their job is finished though, and there shouldn’t be enough residual yeast in the bottle to worry about off flavors from autolysis, it just might be hard to reculture from that bottle. So I think this is another one of those cases where you just need to RDWHAHB. 
Another likelihood is that the sediment isn’t all yeast, but the brown stuff is sedimented malt particles and whatnot.
Regardless, if you don’t perceive a problem, I don’t think you have one.
Words to live by!
Isn’t that brown stuff some of the residual hop isomers that gradually drop out of suspension? IIIRC Jamil Z or Palmer talked about it: such as a brew gradually losing half it’s BU’s over a year’s time due to this process. Ends up as brown sludge in the bottom of bottles or kegs.