Please share the block diagram of your connection for SPI2 with MCP2518FD module.
Have you applied the following patch for SPI driver?
Jetson orin nano SPI Speed not changing - #9 by KevinFFF
Please also share the full dmesg for further check.
You can also check if the clock settings for spi1 and spi2 are similar.
$ sudo su
# cd /sys/kernel/debug/bpmp/debug/clk
# grep "" spi*/rate