I'm assuming a lot here, but looking at the data of what I think you're referring to - I don't see the issue.
Here are the standings for the RL G10 Mojave group. I've added a column to that spreadsheet, with the current rating as of today:
View attachment 14959
The rating tracks to the standing in the conference almost exactly. There are small nuances between #4 & #5 and #8 seems a little low, but in general - it maps pretty closely. Which makes sense, the ratings come from the performance in games. But more importantly - if you look at the history for the #1 team, and look back on their last 20 games, the app clearly shows that they performed exactly as expected 18 times, and underperformed twice. That's a ringing endorsement that the rating that they have corresponds to the results they are seeing because, again, it's circular. They get the rating that they perform at, and they perform at the rating they get. Now look forward, to see what's likely to happen in their next two games. They should beat HB Koge by about 2 goals, and they should beat Pateadores by about 4. Will they do that in either? Who knows. But the app gives them a 62% chance of winning against HB Koge, a 16% chance of tieing, and a 22% chance of losing. Against Pateadores, they have a 78% chance of winning, a 9% chance of tieing, and 13% chance of losing.
So the question is, is that 41.00 low compared to what it could be if they played outside the conference with more challenging teams? Who knows. #1 team in the state is showing a 45.47 in ECNL, and Slammers RL is showing a 41.00 as the #25 team in the state. Considering two months ago they lost 4-1 to Beach ECNL (43.44), and 2-1 to Slammers ECNL (42.39), it doesn't seem terribly off at all to me.