The NYSE issued a "non-regulatory halt" of these securities, which means they will not be trading for the remainder of the day.
Although trading has stopped for these small cap companies at the NYSE MKT, they are continuing to trade in other exchanges.
NYSE told CNBC there were problems with the database of these nine symbols that affected order processing and trade execution. All orders placed on the nine symbols before the market opened will be cancelled back to clients and will not be filled.
"This will definitely affect our company but we can't quantify that yet," said Lloyd Hoffman, CFO of Alpha Pro Tech, one of the companies that saw its trading halted. Hoffman asked NYSE to provide a news release to investors about the halt but said the NYSE declined the request.
"I'm certainly disappointed. You're going to halt trade on my stock and not do a news release? It doesn't make sense to me," Hoffman said. "Our stock is down 4 percent. Would it have been down (without the halt)? I don't know. That's not a normal decline."
Dan Cartwright, CFO of TherapeuticsMD, agreed that the NYSE's decision against a news release was "the most disappointing part of this." About 20 percent of the company's shares trade daily on the NYSE MKT.
"It's not really a halt if you think about it. The shares are still trading in other markets," Cartwright said. "Electronics is our best friend and our best enemy. I'm disappointed it went down, but I don't think it will have lasting effects on our stock."
Shares for TherapeuticsMD is down nearly 3 percent.
NYSE has not yet confirmed when the nine symbols will resume trading, but Cartwright says the NYSE told him trading would resume Friday.