Despite offering to pay above-market rates, investors were unwilling to sell their U.K bonds, known as gilts, to the Bank. This meant that it missed its target for the second round of new quantitative easing (QE) purchases.
The central bank tried to address market concerns Wednesday by announcing that the shortfall would be addressed later in its bond-buying cycle.
Gilt yields moved lower following a statement from the bank, and were trading at 0.540 after the announcement, down from Tuesday's close of 0.584.
While the shortfall of £50 million is small in comparison to the total size of the package, it shows some of the new difficulties facing the Bank and may hasten calls for more drastic action by the U.K. government to combat the U.K.'s slowing economic growth.
Investors like pension funds, one of the major investors in the long-maturity bonds which were the target of Tuesday's auction, are holding on tight to their safe assets. This is partly because of general concerns about the economy, but, possibly more importantly, because U.K. pension funds are facing a record deficit of more than £400 billion.
"It tells you something about investors' anxiety that the bank goes into market and says we want to buy these things from you, we're prepared to pay what looks like a good price, and they get the majority of what they want bought but actually not everything," Ian Barnard, founding partner at Capital Generation Partners, told CNBC.
"I think that tells you that investors...want to hang onto their gilts which are this protection against further bad economic news and further deflation."
For the Bank, and central banks across the developed economies, there are now deeper questions to answer about faith in their capacity to fix the global economy's problems.
"Why does so much of the money that is borrowed via the credit markets just spin round the financial sector, either via buybacks or special dividends?" Marc Ostwald, currency, rates and emerging markets strategist at ADM Investor Services International, wrote in a research note Wednesday.