As I said I cannot reproduce this problem. In the first image below I don't have the PHB loaded and as you see I get an error in chat and the spells don't populate when the NPC sheet is opened. In the second image I have now loaded the PHB; closed and reopened the NPC sheet and I no longer get the chat message and the spells have populated in the NPC sheet. So you must load the PHB before opening the NPC sheet or placing the NPC on the combat tracker. Also if you load the PHB after opening the NPC sheet you must close the NPC sheet and reopen it in order for the spell parsing to work.
There is an issue with certain casters such as the Yuan-ti reported above which have additional text; namely (psionics) after the spellcasting trait name and that is preventing the spells from populating. That is on Moon Wizards list of things to fix in the next ruleset update. In the meantime you can remove the (psionics) bit from the trait name and then close and reopen the NPC sheet to have the spells populate.
If there are other specific instances of spells not populating (and the reason isn't to do with additional text after the spellcasting trait name) then if you can specify which monsters and I'll have a look.