Have there been changes with the caregivers in the child care program? That could cause behavioral changes. For the most part, what you describe sounds like typical behavior for the ages of your children. 18 month olds have tantrums and 3 year olds go through periods of time where listening is not a priority. :)
The thing with time out - especially in a group setting like child care - is that the child is usually not given the opportunity to learn the appropriate behavior by being removed from the group. They are getting the message that they are not worthy of being with others because of their behavior, but no one is really modeling what they are supposed to be doing. Often, time out just leads to more time out in group settings, which leads to more behavior issues because a child's self esteem is effected because they are always in trouble.
Granted, I don't know your kids and it sounds like they are behaving pretty typically. As a former child care/preschool teacher, I have to wonder about the staff stability and discipline practices of the program to make a big deal out of normal toddler/preschoolers behavior. Talk to your older child and see if he can tell you anything about why he's not listening to his teachers. That may give you some insight into the situation from his perspective, which will help you and his teachers figure out how to handle the situation. Good luck.
PS - I can direct you to some articles on Time Out in group care if you think it would be helpful.