Which bootstrap themes are you using? Is it the bootswatch module? If so I believe I have fixed this issue and I can provide an update to the themes to the appstore. The bootswatch module has been updated, but the individual themes need to be updated.
You can download any of the themes from here: https://github.com/mendix/MxBootswatch/tree/master/theme
I will update the themes on the appstores now so that they match the ones in the bootswatch module.
You can also download the bootswatch module and it will have all of these themes as well.
If you still have a problem please let me know.
These themes should contain the fix for the calendar z-index.