I've had a similar problem today. Riding through a muddy puddle, the size of a small lake (4m wide x about 5m), I was almost through when the mud underneath just got deeper and I had to put both feet down in the water and mud.
I then found out that my MTB shoes are waterproof (ish).
From then on it was difficult to clip in and out.
To the extent that I had by first proper 'clipless moment'. Bugger, it did hurt a bit for a while!
All this was caused by a load of gritty mud in the cleats and on the pedals.
This 'lake' has been there since our last rains about 3 weeks ago. Everywhere else has dried up.
Hey ho, it's a crap forecast for the next week so it will only get bigger and deeper.