We think it has to do with reciprocal inhibition and increased long flexor activity, which was eluded to but not discussed at length in the article. 

“As previously mentioned, few studies have investigated the effects of thong style flip-flops on gait dynamics, one of which was the initial study done by the authors at Auburn University in which several gait kinematic and kinetic measures differed between two types of footwear illustrating that walking in flip-flops alters one’s gait when compared to sneakers.”


http://lermagazine.com/article/flip-flops-fashionable-but-functionally-flawed

Commentary on this article from our social media sites:

• Reader: It’s great to see a study being done trying to quantify the effects that flip flops may have. Thanks for sharing.
• The Gait Guys agreed. there are several in the article
• Reader: Russ Brandt When I had mild shin splints from running I noticed that wearing flip flops inflamed my shins