In which case, the patrons were correct - they were being accused of shoplifting. Arguing that the clerk "didn't use that exact word" is frankly intelligence-insulting; even non-white people are capable of reading subtext, and the store clerk's actions after they left proved their interpretation accurate.
The clerk may not have used a specific word, but the owner did. According to the article, the call to the police was to report a "larceny in progress." That's a very exact word. According to the article, also, after the police had handcuffed the couple and searched their bags (and done them physical harm and confiscated the mother's documents), found no evidence of larceny, and let them go (though apparently they did not actually stop following them, nor did they give the mother back her driver's license), the store owner "became uncertain" that there had been a theft. Became uncertain?
The owners' story varies considerably, but one thing they assert is that it was partly at the patrons' insistence that the police were called. Does it sound reasonable that persons accused of shoplifting would ask that the police be called? And sorry, but I really doubt that the clerk who miscounted items was polite about the "discrepancy." How do you politely tell customers that you think they stole something? If, as appears to be the case, the customers are entirely sure that they did not steal anything, there is no polite way to suggest that they did.
Of course it's possible that the whole thing was not racial at the start, and that the patrons were overly sensitive, but the whole incident certainly ended up a mess, and if the store and the police end up with egg on their face, it looks to be deserved.
Of course as usual we don't have all the facts, but one thing that seems odd is that apparently the couple were sent to a changing room by one clerk, and accused of theft by another. Why didn't someone think to ask the first clerk if
she knew how many items they'd taken in? Even if the owners are innocent of bias, one does wonder a little about that clerk. What reason did she have for presuming that they had stolen anything?