I've just completed the upgrade to Lrc 9.3 - so using Lightroom Classic. My camera is a Fujifilm X-T4 and I shoot raw+jpeg and In the general preferences, I've always had the setting "treat JEPG files next to raw files as separate photos" unchecked (and it still is!), however since updating to 9.3, the import process is treating the jpeg file as a separate process.
I inserted a card that I had previously imported and Lightroom recognized all of the jpegs as not having being imported. I processed the card to see what would happen and it re-imported the jpegs with a -2 appended to the file name.
the Fuji is on the latest firmware
Lightroom is running on macOS Catalina 10.15.5
The device is a Macbook Pro 16" 2019 with 64GB ram and AMD Radeon Pro 5300M GPIU
I started having the same issue with the EOS R since the Lightroom upgrade on an iMac. I just installed Lightroom on a Macbook Pro and I was not seeing the issue on import (RAWs and JPGs were shown as a single image).
I then setup a Metadata preset to apply on import (similar to what I do on my iMac) and it is now treating the raws and jpgs as separate images. If I turn off the Metadata preset when importing then the RAW and JPG images are treated as one file as desired.
Any chance you are applying metadata or develop settings on import? That might be the issue and if so I think its a bug.
I was having the same issue on my MacBook Pro (macOS High Sierra) with a Fuji X-T3. I think @KDMizzle hit on something. Turned off my Metadata preset and all of a sudden, it started treating the separate JPEG and RAW files as the same file. Turned back on the Metadata preset and it is continuing to treat them as the same file.