I have the microSD reader expansion card, and whenever I insert a microSD into it, Windows prompts me to format the reader, which always fails. The reader also shows up as a separate USB drive from the inserted SD card. I also cannot eject the SD card directly, instead having to eject the whole card, which then needs to be reinserted before I can use the card again.
MY DIY SD expansion card also has this problem in Windows.
As for the reader showing up as a separate drive, my HDMI expansion card behaves the same way, and I assume this is true for any expansion card that isn’t a USB-C or USB-A card.
How many microSD cards have you tested this with? And have you tried moving the expansion card to other USB-C bays?
Apologies for the late response. Seems like the format issue may be isolated to a single card. It still happens regardless of which bay the reader is in, but other microSD cards appear to read without the popup. The card in question has an image for a raspberry pi, so the format option pops up. I’m assuming that it prompts for the reader to be formatted, rather than the sd card, due to how it’s recognized in Windows
In this case, it really is asking if you want to format the card. To Windows’s knowledge, you inserted a storage device that contains data it doesn’t understand. An SD card containing a Raspberry PI OS image doesn’t use a storage format that Windows can handle. 
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This is correct. I used to have a USB drive with odysseyn1x flashed on it via balena etcher, and Windows would always prompt me to format the USB drive. There is likely no problem with your expansion card or SD card, Windows simply can’t read it.
I have an issue where the micro sd expansion is not discovered and the same thing happens with the expansion card memory stick. Not a big deal, but i have to turn the machine off, unplug the expansion card and put it back in. It will then be recognised on a re-boot. Has anyone know why this happens?
Are you ejecting the SD card?