Telling us what troubleshooting you are trying would help.
There isn't enough information here to really answer your question. What does your installer say? Have you tried to compare those output readings with another device such as the utility meter? What does Enphase production monitoring say? Are you taking these measurements on or off grid?
I would troubleshoot this knowing the following:
There are a few things that can go wrong with a millivolt signal like this.
Try zipping the wires to be measured together to make a more tight bundle where it passes through the CT meter.
Try a different CT meter or the remote meter W2, sometimes the meters are off a bit
Make sure you don't have ANY loads on the wires you are reading as PV generation.
Make sure that where your CT wires are very near other high amperage wires, they are well twisted together. Re-route the CT wires at least 0.5" away from the other hot conductors.
Move your CT's away so they aren't touching other hot wires as much
Make sure L1 is known all the way through your system, and consistent.
Turn off the house loads 100% and compare your PV production to the utility meter reading, then do the same as you turn the PV breakers off one by one.
Make sure that the extension used for the CT's is a proper twisted pair of wires, and does not exceed the maximum length allowed. It's very easy for a tiny voltage drop or interference to affect things in a big way when the whole measurement signal is from 0-333mV
What gauge is the CT extension wire, how long is it?
Turn off portions of your PV while under consistent full sun, and while your house load is completely off and see if you can identify one circuit where when you turn things off, the PV generated. Know in advance what sort of drop you should see when each string is turned off and confirm the readings using the utility meter and the app as you shut breakers off one by one.
After this test, you will be able to tell if a portion of the system is misconfigured, or if the error is a larger measurement error spread across all circuits evenly.
If the error is spread out, the cause is likely a bad CT, or its reading. If the error seems limited to a single circuit, then I might take a closer look at the circuit phasing.
