I brewed on Saturday and noticed after boiling I ran the wort through my chiller and it had maybe a 1/4 cup of clear water/sanitizer before the wort. Will this cause any problems? What about left over pbw? Any worries?
I assume that your sanitizer is a "no-rinse" version. If that is the case, then it is expected that you'll have a little in your batch. Try to think of it in terms of relative volume. 1/4 cup = 2 oz. Total volume is 640 oz for a 5 gallon batch, so you are in the 0.3% range. Even if you had a full cup, I think you'd be fine since the amount is relatively low.
I have heard that left-over PBW residue can affect head retention, but again, it depends on the situation.