I've been having this problem for about two days. It started happening at random and I've not been able to find solution to the problem.
Basically if I try to open a link to a website that has an app on the playstore, Google Now will tell me that it can't find an app to open the link with instead of opening it in Chrome.
I have tried clearing defaults and reinstalling both chrome and Google Now but to no avail. If the website doesn't have an app linked to the playstore it opens just fine in Chrome.
I'm running euphoria on 5.1 if that helps. I'm also rooted.