What game? Someone might have looked at it before or be willing to take a look themselves.
I am surprised emulation is so tricky here. I expect the odd bit of trouble with 3d but 2d should be absolutely fine (it being little more than a slightly jazzed up GBA which has been around for almost 2 decades).
I would look at what is causing that.
Crystaltile2 has not been updated in a long time so most old stuff should go here.
Generally though it has several modes (hex editor, assembly, tile viewer, tile editor and text) plus a load of ancillary tools and things to fiddle with (compression formats, relative search for text, various font handling and generation -- try typing on the tile viewer). Menus change with what mode is selected. In addition there is a little DS icon on the right hand side. This will bring up the breakdown of the DS ROM (it has a filesystem, unlike most things that did not come on a floppy disc or CD before it) where double clicking will set the tile editor/hex editor/assembly viewer to that location. Right clicking will allow you to view the file if it has a format it supports/recognises (has many, tinke has a few more but more revolves around those formats rather than being ROM focused) or handle any compression.
Do note that many DS graphics formats will be split between the graphics, any animation and the palette side of things. This can make handling compression a bit more tricky (I usually make a new ROM with all the uncompressed files plus helper files I want to look at and go from there)
Anyway even if it does not support the format you might still be able to get something done.
The tile viewer is one of the best we have. The configuration options are on the left hand side and should be reasonably obvious. The main options you will be using with the DS are tile sizes (while most old consoles are content with 8x8 and 16x16 or some combo of those, maybe with a narrower one for the odd font the DS can have tiles/graphics going right up to full screen resolution and often does. The graphics viewer, OAM viewer and the like might give you some idea what to be looking for here as well) and graphics format (different devices do it differently, in this case GBA 1bpp (usually more for fonts), GBA 4bpp and GBA 8bpp will be doing most of the lifting for 2d stuff. There have been some cases of 3d acting as 2d (make a simple flat square and put a texture on it) and in that case you do have another graphics format that will want another tool like tinke or maybe tiledggd.
ctrl and arrow keys and maybe shift and arrow keys will do fun things, as well as arrow keys in general.
For palettes then for crystaltile2 if it does not support it in the nds viewer part you get to find it in the ROM, or maybe rip it from a savestate. To convert random data to palettes you will need to go to the hex viewer and there will be an option along the lines of hex 2 pal and pal 2 hex which do much as they say, try not to edit your ROM accidentally as it will indeed dump the palette right where the cursor is if you press the palette to hex option. There are options to bring in windows palettes and export as well, also bring in and export BMP and PNG if you want to edit outside or simply export.
Finding things can be time consuming.
https://www.romhacking.net/documents/361/ is for the GBA and for a command line tool where today no$gba's debug version is probably the better bet (might also be an option for your grabbing efforts). Still it, (
http://problemkaputt.de/gbatek.htm#dscartridgeprotocol B7 commands are for the ROM, work backwards to figure out what it reads*) is the best method that will work every time, though it is complicated.
Less complicated but more time consuming is looking at file/directory names, file sizes and extensions (sound_data.sdat tending to be sound and thus of no interest to your graphics finding, also a nice chunk of most DS ROMs eliminated in one shot), arm7.bin usually being a helper file common between DS ROMs (as in you can swap them between ROMs of similar age and have everything work just fine) but ARM9 and overlays being the binary which can house things in some games.
You can also simply load a tile editor and press down a lot.
Corruption is also a thing. Corrupt part of the ROM and see what changed in the game. A lesser version of this might see you copy and paste over the parts of the ROM -- files with similar extensions might be good as one working will usually see another still work for it but maybe have different data (think overwriting a file with the name of the main character with that of the sidekick and seeing the sidekick now appear as the main character), as you know what you changed (or maybe what it was trying to load when it crashed) then you know what goes.
*crystaltile2's hex editor and possibly tile editor will say what file in the DS ROM the cursor's location corresponds to down the bottom if you would rather not go manual with the results of ndstool, ndsts
http://www.no-intro.org/tools.htm or similar.
Anyway it seems I am now writing a basic guide to graphics hacking which I already did
https://gbatemp.net/threads/gbatemp-rom-hacking-documentation-project-new-2016-edition-out.73394/ (also includes some usage on crystaltile2) so I will cut it off.
