This is in a March to October HoF difficulty game.
I use classic baserunning and almost never have issues unless a player rounds a base and their button changes. This is a design flaw in the control scheme and either needs to change or an alternate control scheme created where a runner keeps the same button regardless of where they are on the base paths. (Classic Static controls).
Notice what happens at 0:08 on the bounce: I decided to send the runner from 2nd to 3rd and hold the runner at 1st.
Problem is the runner that was O is now triangle and batter (X) is now O. So when I press O and d-pad left to send the runner from 2nd to 3rd I'm actually sending the runner from 1st to 2nd (as he can't go to 3rd due to the runner ahead of him). And when I press X to select the batter to send him to 2nd, nothing happens). So the runner on 2nd stays on 2nd and the batter runs to 2nd.
There's also a bit where I seem to have decided to send the runner from 1st back to 1st as he makes it to second, according to the base paths HUD. It is possible that I double-tapped the buttons to select a runner (a habit I formed after playing some online games because a single tap doesn't seem to work online) which could have contributed to the problem.
Then on the subsequent rundown, my plan was to send the batter back to 1st and give the runner on the 2nd/3rd base path a chance at being safe (managing two runners). However once the batter reaches second, I can't send him back to 1st to try and avoid the out. So the runner on the 2nd/3rd base path is out no matter what happens.
Admittedly this is user error and I take responsibility. However the interface can be made more user-friendly by not changing a runner's button as they round the bases and allowing a runner to return to the previous base if they are selected.