MATLAB/Simulink can be stuck in busy for a while after running on the target with File Log blocks, depending on how much data is logged to the File Log blocks. For large amounts of data, it simply takes time because downloading the files back to the host can take a while.
One way to workaround this is to turn off "AutoImportFileLog".
In R2021a and later this can be done by starting the simulation from Simulink Real-Time Explorer and unchecking the "AutoImportFileLog" box, instead of starting the simulation from the Simulink window.
Prior to R2021a this must be done by starting the simulation using the "start" command in the MATLAB command line and setting "AutoImportFileLog" to "false". For example, if the target object was in a variable called "tg" and the model was called "model" then you would use the following command:
To learn more about how to use the "start" command visit the following documentation link: