Temporary closed signage is seen at a store in Manhattan borough following the outbreak of coronavirus disease (COVID-19), in New York, March 15, 2020.

The government's nearly $350 billion loan program for small businesses officially ran out of funds on April 16, even as many American business owners are still struggling to make ends meet or plan for an uncertain future amid the coronavirus pandemic. Congress and the Trump Administration continue to negotiate on adding another $250 billion to the first-come, first-served program, which has seen over 1.6 million applications even as criticisms have mounted over delays and confusion in the application process. Holly Wade, the director of research and policy analysis for the National Federation of Independent Business (NFIB), the country's largest small business association, tells CNBC Make It she's heard from countless small business owners with concerns about the application and payout process for the Small Business Administration's [SBA] $349 billion Paycheck Protection Program [PPP]. "The list of frustrations is long," Wade says, noting that many businesses had trouble finding bank lenders to accept their applications, especially if their personal bank wasn't participating in the SBA's program, after the application process kicked off at the beginning of April. In fact, many small businesses across the U.S. that have already been approved for loans are still waiting for money to actually hit their bank accounts, while others are worried that strict guidelines over how they can disburse that money could ultimately do more harm than good to their business. Wade sums up one of the most prominent complaints she is hearing from small business owners, who tell her: "'I've applied and I have no idea when I can expect the loan to be deposited, and so I don't know how to accurately adjust my business operations based on declining sales and keeping the door open,'" she says. One small business owner who is still waiting for his loan money to come through is Lyle Butts, the 73-year-old owner of Bay Sails Marine, a boatyard and marine supply store located on Cape Cod in Wellfleet, Massachusetts. Butts has been running his business for five decades, so he says he's survived numerous financial crises in the past. "This is, kind of, not my first rodeo," Butts tells CNBC Make It. "But, certainly never anything like this before."

Butts started the application process for the SBA's PPP loan over the first weekend of April and he estimates the process likely took roughly 20 hours of work from himself, his retired wife and one of his business's eight employees. What's more, he had to enlist the help of his longtime accountant (a factor that will likely end up costing him up to $500 in fees on its own, he estimates) to go over the company's financial records and ensure everything would be in order for Butts' loan request of roughly $50,000, he tells CNBC Make It.

Lyle Butts has run Bay Sails Marine in Wellfleet, MA since 1970. Source: Bay Sails Marine

Butts finally submitted the application to his bank on Tuesday, April 7, nearly four days after he'd started the process. He claims his bank approved the request but, as of Friday morning, the funds had still not been deposited in Butts' account and he had yet to hear any word from his lender or the SBA on when he could expect to see the money that he says he'll need to keep his employees paid and his business afloat for "another couple of months." Butts is adamant that he's not looking to lay off any of his employees. Because Bay Sails Marine is a part of the transportation industry — it offers boating storage and supplies — the company has been deemed an essential business, which means Butts can still keep operations running, but business has still dropped off. The company, which typically brings in between roughly $1 million and $1.5 million in annual revenue, has seen its business drop off by about 50% amid the coronavirus pandemic, Butts says. For that reason, Butts is relying on the loan coming in sooner rather than later. "We put some money aside and we're good for awhile yet, you know, we can keep the corporation running for another month," says Butts, adding that after a month, without loan money coming through, he would have to start dipping into his retirement fund to keep paying his employees. "And, I just can't do that." "You know, I'm at the age where I don't have a second shot here," he says of the possibility of replenishing his retirement fund should he need to use it as a financial resource. U.S. Treasury Secretary Steven Mnuchin and SBA Administrator Jovita Carranza issued a joint statement on Wednesday urging Congress to "appropriate additional funds" for the PPP loan program, as the SBA is now no longer accepting new applications with funding running out. And despite some criticism, when reached for comment by CNBC Make It, an SBA spokesperson touted the fact that the SBA "processed more than 14 years' worth of loans in less than 14 days," in a nod to the massive size of the undertaking that has been the PPP program. "The Paycheck Protection Program is saving millions of jobs and helping America's small businesses make it through this challenging time," read the joint statement from Mnuchin and Carranza. However, even as small business owners like Butts play the waiting game with their approved loans, others who have access to their borrowed funds are now concerned that the guidelines around their disbursement might not actually be in the best interest of their business. For instance, Agatha Kulaga, co-founder and CEO of the small New York-based bakery chain Ovenly, made the difficult decision to temporarily lay off all of her company's 67 employees, herself included, after shutting down operations at Ovenly's four retail locations and one commissary kitchen on March 16.