ACF is a great tool, and I wouldn’t use anything else, but it does have its limits. I created a site with a field group that would actually time out the server. Since then I’ve found that limiting how many fields you add, especially when it comes to some types of fields is a good idea. In your case I would break the group down to multiple options pages and group the fields logically.
The problem is not really in ACF. The problem is in WP. WP does not have any way built into it that allows updating multiple meta fields or options values in a single query. Each value to be updated creates several db calls and at a certain point the number of db queries drags down the page speed.
As far as fields not saving properly, James is most likely right that this is caused by going beyond the max_input_vars php setting on your server.
