As I surmise, there's no public source code for shogidokoro and this is the only way to report issues, so excuse me.
1. Shogidokoro manages engines using full exe path as a key in almost all places. This is an issue if you have the same engine with different configurations (e.g. different NN models/books/tweaks). This makes it impossible to run engine vs engine games on the same PC, and is especially annoying for tournaments (you can do p2p game with 2 shogidokoro instances, but that has its own issues with auto game save).
2. Every time shogidokoro loads an engine, it updates the engine profile name using the name provided by the engine. This is a similar issue to 1., as it can be hard to distinguish between different configurations. Suffix option is kinda useful, but is very limited in length in UI (though you can edit engine.xml manually without issues), but some engine names are quite long and most dialogs in shogidokoro are not resizable, which makes it impossible to select proper engine configuration sometimes.
So shogidokoro should use engine profile ID instead of the engine path alone, and there should be an option for custom engine name, and suffix length limit should be removed or at least extended to a reasonable length.
3. Shogidokoro always sets USI_Hash option even when engine doesn't have it (e.g. dlshogi_tensorrt), which makes some USI engines unusable. Shogidokoro shouldn't set options not reported by the engine, and preferably, if current value is default (this will help if the engine has removed settings after update too).
Now the rest are more of a user experience issues than real bugs.
4. Game log notation in UI is language-specific, this should be an UI option, with Auto being the default value to preserve current behavior if desired.
5. Score graph range is ok for human games, but for engines having 5000-6000 difference is normal, so the range could probably be expanded, with optionally changing the combobox to have user input with current values pre-defined.
6. It would be nice to have an option to save tournament configuration/progress, so you could interrupt and resume at a later date (stopping mid-game, or at least between pairs).