The M3 perfect was pretty much one of the most sought after gba flashcarts around for gba pokemon players, I have rarely seen anyone say that their M3 perfect didn't work.
The closest analogy to what this issue is, is like the dyes used in DVDs and CDs and what disc drive you had. Crappy DVDs and CDs with crappy dyes tend to not work or over a short period of time stop being able to be read by one drive but works in another one of a different model.
And then you the intention incompatibilities. Like between different manufacturers of certain products. Example of this is DLink and Cisco, where Cisco routers and switches detecting any DLink hardware like other switches, routers or network cards would intentionally introduce intentional errors or drop them from that node in the network, or refuse to communicate with DLink hardware entirely. This was done to be able to claim DLink hardware was inferior and should be dropped from any customer hardware list and go with Cisco only hardware.
Examples of other GBA flashcart incompatiblities include the following
EFA and nForce motherboards or motherboards with certain USB controllers
Incompatibility here was the USB controller didn't like the USB controller on the EFA flashcart.
F2A and P25 ports
Incompatibility here was if your P25 port didn't support a certain mode, it would never detect your F2A flashcart. This only happened with REALLY old motherboards.