The Protocol Designer is telling you something may be wrong, but technically the robot can perform the instructions you gave it. These are dismissible.
Example: You can tell the robot to try to aspirate more liquid than exists in a well according to Protocol Designer's liquid tracking.
Errors will prevent the robot from running your protocol. In fact you probably may not even be able to upload it to the run app. These are not dismissible, but you can download files with errors.
Example: You cannot tell the robot to try to aspirate liquid with no tip on the pipette.