The nice thing about encap is its unique ability to remedy situations other methods didn't. It sells itself when you're the third or forth cleaner to try, the first one to think a little outside of the box, and the only one to make the problem go away. Over the years we picked up quite a few accounts that way, encapping the problem area only one time. It worked great, removing things like drink and mop bucket spills, and it didn't foam during subsequent visits.
We've been using encap products for twenty years. We don't do much straight encapping but we do a fair amount of residential and commercial pad-capping. Never seen or heard of a single problem related to encapping or encap products left in the carpet.
While it might cause foam in the waste tank, in the carpet, it continues to do what it was designed to do, encapsulate dirt.
Back in the day, we used to refer to it as the Poor Man's Protector. It provided some level of protection against resoiling. Theory held dry soils stuck to the remaining encap, not the carpet. Wet soils mixed with the encap residue, drying and encapsulating at least some of the soils
If it's not causing a problem and affording continued resistance to soiling, I'd suggest that's a benefit, not a problem.