At least in my software are primarily intended to reduce etching costs thus they are intentionaly separated from all placed objects.

You may have to add a connecting trace forcing the desired connections.

I error check to no errors then add the desired fill to ground plane via connections. Set the error checking to ignore these errors if possible and manually confirm that there are no errors or missed connections due to this forcing of the software. If your software will not allow you to control the error checking just confirm that all errors reported are intended connections. Again it is your responsibility to check the final output for errors.
Note that in this approach if you fail to connect a via the software will not catch it.
Terry