I used to do scuba diving and I used a small echo sounder/fish finder on my boat. It will show reflections of the seabed (lake bed) but it will also reflect off bubbles — including the swim bladders of fish.
When there are divers down, the air they breathe out forms large bubbles which the echo sounder treats as large fish. All the echo sounder is doing is showing an echo, rather than correctly identifying the target.
Therefore, a cluster or stream of bubbles may show up as a long continuous shape, and as the bubbles ascend at different rates depending on their size, and the small ones can merge, the shape changes, and may also dissipate — making the target impossible to find on a second or third sweep of the area.
Bubbles can also be released by decaying matter on the sea bed/lake bed, often in short bursts.
Also, a large dense shoal of small fish may sometimes cause a compound reflection that may be identified incorrectly as a single large target.
There are also occasional pieces of debris and weed that are more or less neutrally buoyant that can hang about in mid water, ether slowly ascending or slowly descending. Deep water is not consistent in density due to layered changes in temperature, salinity (in the sea or estuaries, rather than Loch Ness) or particulates in suspension, so an item of the right density may be positively buoyant in one layer and negatively buoyant in another, and be temporarily trapped at the boundary. There will be a lot of sheets of polythene, old feed sacks and that type of thing in the loch.
I've read the article in the link. There is certainly nothing here to justify concluding that it was an unknown species of megafauna. My guess is bubbles from decaying matter.
Either that or a traffic cone thrown in there by a bunch of students as a hilarious jape.