In the Bedrock Edition of Minecraft, nether portal blocks do not get waterlogged properly. This occurs with both the individual portal block and when naturally built with flint & steel and obsidian. The result of this glitch is an air bubble and a cosmetic flaw. This also occurs with end portal blocks as well. It is cosmetically unattractive and it also is inconsistent with the behavior of other non-standard-full-sized blocks such as fences, end rods, half-slabs, etc.
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However, this issue has been closed as Invalid.
This behaviour is actually the same as the Java edition. For suggestions or feature requests, please visit the Minecraft Feedback Site or choose a link below.
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Confirmed in 1.10.0.4 using Windows 10.
A portal block placed using the /fill command does not become waterlogged when placed underwater. This differs from fences and other transparent blocks placed this way, which become waterlogged.
Note that this is probably by design. When water comes into contact with a portal block in a nether portal, it extinguishes all the portal blocks, so the notion of a waterlogged portal block has likely never been treated as possible in the code.