Let me first say that this is not legal advice or opinion to any party with an interest in this, but just me giving a general overview on US trademark law and how I think it could apply here.
Unfortunately, what specific TM rights regarding "Cascadia Cup" are owned by who is not so straightforward. Trademarks are a really messy piece of intellectual property in general because trademark rights attach in common law with use and consumer identification. These rights can shift over time and be vested and lost regardless of the actual registrations, federal or state. For example, the famous marks "Singer," "Xerox" and "Rollerblade" have constantly had to fight against losing their trademarks for becoming "generic" and simply descriptive of a device or action. Likewise, poor licensing and control can cause a trademark originally owned by one party to shift to another because the consumer in the channel of commerce for the mark identifies the licensor as the owner of the mark.
So right now with the Cascadia Cup, this "shifting" could be a big problem. If one were to ask people in the US outside Cascadia what is the "Cascadia Cup" in soccer, chances are they would identify it with MLS, and not the supporters groups or the USL. The MLS could argue that because supporters groups let the MLS use the term Cascadia Cup over the last two years and did not "police" it, the TM rights have switched over to MLS. A duty one has with trademarks is to police against their usage by others, and the SGs haven't done that--not that they knew they needed to. But now, MLS has staked a claim and this issue has become ripe.
One has to also note the use of the trademark, e.g. "entertainment services, namely, annual series of soccer contests among professional soccer teams," like MLS claims for its use of "Rocky Mountain Cup" since 2005, versus the actual, physical Cascadia Cup. There can be different TM rights here between the actual display and award of the physical Cascadia Cup, and the "soccer contest" called the "Cascadia Cup." The supporters groups did not actually host or provide the soccer contests for the CC. So you could have the bizarre scenario where the MLS has the rights to host a soccer contest called the "Cascadia Cup," but may not be able to physically award or call the award a "Cascadia Cup."
If you think about it, how specifically were the supporters groups using the CC term in a trademarking sense to identify a good or service? Maybe selling support group memberships? A way to provide support and supporters for local soccer clubs? The determination of what goods and services the SGs provide (and have provided) under the CC mark is key, yet not very clear.
Another issue to creep in is the geographic use of the "Cascadia Cup" mark in that the supporters group may have superior rights to the CC mark in Washington and Oregon, but not in the rest of the US. Federal trademarks can have geographic limitations.
Given how murky this really is, one can see why MLS jumped into the sandbox and is trying to yank the toy away screaming "mine!" Needless to say though, it doesn't look like MLS can get all that it wants for the "Cascadia Cup" mark without striking some type of deal with the supporters groups.