scruffy, it sounds to me like a shallow water table problem. the way i see it you have two options:
1) continue to fill on suspect area (and lose depth) until you can get a firm compaction
2) get a backhoe in there, strip out the good clay you've brought in and save it, dig a test a hole in the suspect area to determine the geology (is it a groundwater containing sand, rock or silt, is it a local perched zone or part of a more extensive water table??)
you may find you can dig deeper, get to a hard soil horizon, and then seal it off with imported and compacted clay. if this is the case you will have removed the slushy soil, and then can and likely have to pump water out to keep it dry enough to work on.
on the other hand, you may find it continues as a saturated slushy soil horizon, and you have to seal yer pond well above this layer. it is hard to give advice on how to seal a pond when you dont know the deeper geology.
FWIW, welcome to the world of leaky ponds (i have one) and GOOD LUCK.......
edited post.....i should have mentioned as eric pointed out (posting at same time
) the obvious near future option is to see if what you have done is sufficient....if it leaks out, then you are faced with the two options i could think of posted above. as i understand it, the bubbles are usually organic gasses trapped in the soil and being released as the soil "wets" or becomes saturated by the new pond water.