I also used crinone until I was 11 weeks, and I also had some days where the color looked a little tainted (either pinkish or brownish). I think that's pretty common. As for still seeing the gel when going to the restroom, I'm guessing you never removed any with your finger? It can really build up, and for some reason, Crinone tends to get kinda stuck up there...so maybe just use a finger to gently remove any leftover gel next time you take a shower. That's what I did. I was actually instructed by my RE to remove leftover gel every 3 days or so while on it, and there would always be a whole bunch stuck up there :-)
I would not be concerned at all. You can bring it up at your next appt. if you are worried.