Check your hardware before checking your code...

Unwanted resets

The watchdog isn't reset often enough, write a byte to REG_DIPSW at least each frame.
An exception is occuring, set up a simple 68k exception handling screen to debug your code.
Misaligned word or longword read/write (address error)
RTS with wrong return address in stack (or bad SP ?)
JSR instead of JMP
Jump table with bad index (address error)
Timer interrupt too fast, causes stack to explode

Invisible sprites

Sprites are disabled (NeoGeo CD only, activated by default)
The fix layer is filled with non-transparent tiles and hides everything. Clear fix with tiles filled with color 0.
Sprite position is out of the 320x224 visible area.
Sprite height is set to 0 (SCB3).
Sprite tiles are all transparent (bad tile numbers ?).
Tile colors are the same as the backdrop color
Shrinking values too low (at least one pixel should still be visible).
Bad C ROM, it happens...
Reference color (0) is not black.

Sprite is driven by the previous one.
REG_VRAMRW or REG_VRAMMOD writes too fast.
Never use CLR instructions on LSPC registers.
The Timer interrupt routine has VRAM writes which interferes with the VBlank interrupt routine. Disable the Timer interrupt when out of the display area.

Some emulators ignore the timer interrupt, it may work on the real hardware.
The interrupt mask causes them to be ignored by the 68k. Check the SR register.
Wrong configuration of the timer interrupt, see REG_LSPCMODE.
The interrupt vector points to an RTE or RTS. Beware of the different levels between cart and CD systems.

Stop the timer interrupt when out of the active display. The timer interrupt can be very mean.