I'm observing the same behaviour here with different braces and quotes (with current 1.29!). In my opinion it's quite obviously that the feature from auto-close plugin is conflicting with the Geany builtin features.
At this point I don't understand what exactly the auto-close plugin is doing different than Geanys builtin features, but I guess most likely there is a difference? Why would someone re-implement this feature as a plugin if there wasn't?
However, the plugin should check if Geanys builtin feature is ticked for the following and then disable (grey out) the tickboxes for parenthesis, curly brackets, square brackets, single quotes and double quotes. To manually tick and untick is…well…you have to move from keyboard to your mouse, you know…