Hi @Abhiram_m_s,
You need to review your clocking configurations from the LLCE side at your M7 core.

[page 2768, S32G3 Reference Manual, Rev. 4, 02/2024]
For FlexCAN with the A53 Core review the following:

[page 2619, S32G3 Reference Manual, Rev. 4, 02/2024]
Reviewing the Clocking chapter of the RM.

[page 921, S32G3 Reference Manual, Rev. 4, 02/2024]

[page 918, S32G3 Reference Manual, Rev. 4, 02/2024]
As you can see LLCE and FlexCAN shares the Clock for transmit you need to review your configuration of each module to use the same prescaler to match the frequencies in both transmit options.
Some other important information to know here is where this clock is generated:

[page 1346, S32G3 Reference Manual, Rev. 4, 02/2024]