I created a GND polygon on the top layer. It's connecting all GND nets except few ones. I am including one net that's not being connected to the polygon below
Now, if I change the Net options in the Polygon Pour window to Pour over all net objects, it works.
I don't know if I can do that and if that's a problem. Thanks!
Yes, can do that; you just did. It's only a problem if it's not what you want. It's really unclear what your problem is. Your image doesn't show what you expect to be connected that isn't. Maybe your problem is clearance: there's not enough room for the copper to pour between elements?