More than likely that plugin only supports the free version of ACF.
If there’s a problem with ACF4 on multisite you can either submit a support ticket https://support.advancedcustomfields.com/new-ticket/ or you might try opening an issue here https://github.com/elliotcondon/acf, either of these should get the developer’s attentions. I’m not too sure about ACF4 on multisite and I don’t see any reason why it would effect the link options in WP.
I’m not going to be much help with that error, that’s something you’d have to take up with them I think.
