Are you using "execute command immediate" type? if you use them & send a character to a specific position & tell it to wait until character stops, it doesn't actually listen out for when the character arrives at the destination, but for when the character stops in general. You need to wrap action parts for immediate actions in begin/end cutscene or hide/show cursor action parts to disable player interaction.
Though the better solution is to use "at destination" type commands. Set object position & alignment in the objects properties section & when you click on the scene object it will walk to the specified position & align itself automatically, & better yet, if the player sets a new destination while the character was walking to the other object/character, it won't execute those actions because they only execute when the character arrives at the specified destination.