I have found two separate issues regarding town ports.
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If you used town portal to return to town, while in town you can open a second town portal. If you return through the first portal you are taken back to the zone you left off in. However, if you enter the second portal you are taken to another instance of the same town. This town will have a return portal like normal, upon entering takes you to another instance of the same town except your original portal from the other zone is now gone.
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You can submerge portals into the ground if your mouse is hovering over terrain that is “lower” than your character. For example, if on the upper ledge in the end of time, you hover your mass over the distance lower levels the portal will go into the ground and only the top of the portal will be visible.