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If you have any mods installed those can prevent proper operations of the game, or they have conflictions, or unfinished data. As for save files, aside the autosave, you have to save manually in the options tab and make sure it is an original character as your secretary, or you can have issues with the save icon.

This is a bug and has been patched in v0.1b

If you're messing with mods it is possible for the game to crash by assets not being present or unidentified. If you're not using mods try reinstalling a fresh copy of the game

If you don't mind sacrificing units, you can also attempt to put her to sleep with Dusk Lamia, just make sure you have enough room for Dream Eater to kick in

To my knowledge, the most recent build is v1.0b

The creator did state she'll eventually become an option to be an ally

Yes, there are new characters planned, currently the new ones seem to be goblin girls (and possibly elves following that), it is unlikely you'll be able to increase capacity of the original unit without modding it. As for the shopkeeper, it was stated that she might become playable in the future under the condition of "becoming a valued customer"