Not Enough Employee Permission
Too many of the options in Employee Roles include too many things. For instance, if I want a manager to be able to add employees to her location or be able to edit clock-ins (say one of her employees forgot to clock in), I have to give her access to Employee Setup. Well, the problem with that is now she can edit her own permissions... so she can do whatever she wants. More than that, she can now edit MY permissions. This is obviously a problem.
A lot of the permissions are this way; all or nothing. Like reports, say I want an employee to see a certain report like check how they're doing on sales for the day. Well, that means I have to give them access to ALL reports. It's just too much.
On the topic of sales. If an employee is locked to a location, then there is no way to give that employee permission to view sales at any other locations. So, if they need to do a return, but the customer doesn't have their receipt, they have to call the other store in order to get the transaction number.
Lightspeed introduced a tool about a year ago called "Sales History," where an employee could look up specific sales from another location, but they recently bricked that tool by limiting visibility only to the store which they are locked.
A permission is needed to be able to see sales at other locations, but not be able to ring sales in that location. Because the only option now is to allow an employee access to all stores. Well, that's a nightmare because now we have employees accidentally clocking in at the wrong location or accidentally ringing sales in the wrong location.
Overall there just needs to be more thought about the permission options.