I've noticed an inacurracy in Altirra 2.80. When I changed DL during the display of the frame Altirra hasn't crashed but on real Atari the code crashed.
edit: unfortunatelly I cannot provide any more information, because I haven't got this bug in my files, and I can't remember what exactly was happening.
This is not nearly enough information to assume it is an inaccuracy in the emulator.
There are many reasons this can occur that are completely correct behavior. For one thing, there is a main division in the XL/XE line between models that have a floating data bus and a pulled up bus. Both are emulated, depending on whether you select 800XL or 130XE as the base hardware. If the display list fetch extends into the hardware region, this can then depend upon what hardware you have occupying the cartridge control region ($D5xx) and the PBI regions ($D6xx and $D7xx). Then, there is usage of uninitialized memory, the contents of which depends both on the type of RAM chips that you have as well as the loader that you have used to load the problem. Finally, the exact timing at which the program starts will influence when the display list is switched and exactly what garbage data ANTIC reads. Unless you are running your program directly from a cartridge, it is almost certain the program will not start at the same beam location.
Long story short, it is not reasonable to expect that the emulator will show you the exact same results as your physical computer in all cases, especially when it isn't configured identically. Like running on a second computer, running on the emulator in one configuration does not rule out all possible failures. However, the emulator does make it easier to try many configurations, as well as diagnostic modes that are more likely to reveal specific types of common problems.
Finally... this is the 2.90 thread, so if you actually did mean 2.80, it is time to upgrade.