How does united.com choose to list award flights?
Departing in the next few days PRG-SFO trying to get LH first (O class FRA-SFO) and it's available.
I'm trying to go to PRG-FRA the day before so I enter that date and tons of stuff comes up. In fact, 198 options. Now only about 10 or so are option in first.
The one I really want, which shows on Expert Flyer, is this.
Day 1 PRG-FRA 2pm-3:10pm (I class)
Day 2 FRA-SFO 10:35am-12:50pm (O class)
The above flight does not appear on united.com and it prices at 18,000 more miles as it is requiring point to point.

So what I really want to know is why does united.com offer these flights? It would seem more flying, more cost, etc.
And by the way, the Day 1 PRG-FRA still shows I9 which is much more full than the flights it is offering PRG-FRA.
Here are some examples it is offering.
Day 1 PRG-MUC-FRA - all in I
Day 2 FRA-SFO O class
or
Day 1 PRG-WAW-FRA - all in I
Day 2 FRA-SFO O class
or
Day 1 PRG-BRU - all in I
Day 2 BRU-FRA (I) FRA-SFO (O)
or
Day 1 PRG-ATH - (I)
Day 2 ATH-FRA (I) FRA-SFO (O)

In my case, even though PRG-FRA shows available in I, whether looked at PRG-SFO or PRG-FRA in I and then FRA-SFO in O, united.com nor 1K reservations can book it without charging more miles.
Instead of flying 256 miles PRG-FRA it is suggesting PRG-WAW-FRA for 876 miles or PRG-ATH-FRA for 2097 miles.

I find it confusing and odd.

First, it is the partner that first determines availability, not UA. And partners may limit how their segments are combined with other of their segments (one way is married segments). This including requiring or restricting how segments are stringed together.

And UA will not allow you to individually select segments and string them together -- include the flight operator restriction. It has to come up in the search naturally.

Best not to try to apply logic (or using distance or cost as the metric) to understand airline bookings. There are things unknown to you and us impacting the choices.

For the same reason AAA-CCC is twice the price of AAA-BBB-CCC. Airline pricing is typically inversely proportional to cost. Here's a great intro to RM.

Also some partners, particularly LHG seem to be dumping premium cabin space on the award market while UA seems to be much more restrained about it -- looking at routing changes for our flight home last week, for example, there were LH F options that would have been significantly cheaper (miles wise) than the UA saver J we were confirmed in.

The quote from that exercise that my wife posted on Facebook: "Wow, there are some really interesting routings we could take if I didn't enjoy being married to you"

My guess is that LH RM has figured that those seats are unlikely to sell and a butt in the seat with some revenue (whatever UA "pays" LH for the redemption) vs. letting the inventory spoil where UA would rather let the inventory spoil on the basis of preserving exclusivity/having space for last-last minute bookings, etc.

Airfare isn't priced on a cost plus basis. Hasn't been since 1978 in the US.

United.com is not good at the ones that require an overnight somewhere. Calling can work to get these booked. You can also try to force certain stopover points in the advanced options or try the app which might give additional ones.