Broken UA IT at its finest. I can replicate this for the most part. The good news is the fare has come down to $1219 now for the W fare

BTW, I did figure out part of the issue but I can't tell you why it's happening. The "W" fare listed at $969 (remember, the price has come down about $60-70) is actually a correct round-trip "W" fare when using the same fare basis. However, after selecting the outbound and return flight they are restricted from being sold under the cheapest fare basis (I don't know why). The outbound is sold as WHX38RCT while the inbound is sold as WKW38RCT. The former has a round-trip fare of $565 while the latter has a round-trip fare of $768. It appears United is combining these fares to make the price what it is.

The applicable days of the week these fares are valid is what is killing you right now. The WHX fare is valid Mon thru Weds only while the WKW fare is valid Tues thru Sun only. I don't disagree that United.com should be smart enough to realize the return is valid on a different fare basis than the outbound and show you what that price would be before selecting the flight.

You may be able to get a cheaper fare if you play with your dates. For example, returning on 9/10 lowers the fare another $30-40.

-RM