If every cell has a shower they should all be using them during the Lockup time after sleeping, certainly during the Shower time and probably during the Free-Time if the Hygiene need is critical.
If some cells lack showers then put Shower immediately after Sleep so everyone should either shower in their cell or go to the communal shower. If you want to have Lockup time to improve your Punishment grading you can have this later in the day after primary needs have been satisfied.
Are all the showers properly connected to the water supply? A flashing blue icon indicates a broken shower. Remember that the small pipe has a limited range before it loses pressure.
Also if some inmates don't have a cell shower are there enough shower heads in the shower room, is the room properly labelled and does it take too long to walk there in the time available?