This is just a quirk of Goomba [Color]. The short of it is, you must press L+R to open the menu and wait a second for games with 32KB SRAM to save properly.
For the long of it is, Goomba (along with PocketNES, SMSAdvance, etc) were all written to support maximally using the space on the 64KB space of GBA flashcarts. However, they also originally (due in part to being based on PocketNES) have an 8KB SRAM block that's written to directly in the 64KB space. So, games that use 8KB SRAM or less on most the emulators have saves that just work. When it was realized that this wasn't enough for some, the solution was to just have SRAM saved/restored on the L+R menu which at the time was something you did anyways to exit the emulator.
At this point, though, some of the emulators (like some of my forks IIRC) have fully abandoned the whole 8KB SRAM area carved out of the 64KB because there's little reason to have SRAM that works some of the times. Better to just require L+R and a one second wait for it to always work. I don't recall which emulators or forks this apply to of the PocketNES lineage, but it's just general good advice.
So, if you are pressing L+R and it still isn't saving properly, then that's an actual issue.