Let's try and step back from agile/not agile...scrum/not scrum perspective.
Breaking this down simply, if they're getting work done but just not getting done as much as they thought they could, I think that's pretty normal. Estimating in a room with other people of all perceived skill levels causes us to try and overestimate to compensate for our inherent insecurities.
If the team is getting things done, try and focus more on keeping the work interesting for everyone on the team and make sure everyone is having fun.
If the team has a clear vision of the project, then you could move to using the stories more as a tracking mechanism instead of "commitments". This would give you the ability to track velocity and estimate project completion time, while not destroying moral of the team.
From an economist perspective a worker could just commit to a single, easiest, lowest point story that's available each week to maximize the chances of them meeting the goal.
The way to counter this is really to try and keep people excited about what they're working on. Even if it's a mundane task, try and pay attention to what motivates each member of your team and even meet with them individually and ask them what would make them more excited about the project.
Just my $0.02. I've been a software engineer for 12 years and I've spent a lot of time working with PMs to help them solve this exact problem.