Others are facing reductions in welfare payments owing to the income received by releasing the funds.
The so-called pension freedoms began in April 2015.
Since then, anyone aged 55 and over has been free to withdraw as much as they like from their pension pots, subject to income tax.
A report by Citizens Advice looked into the cases of 500 people who have accessed their pension pots.
Of those, 9% had unexpected tax issues and 6% found that their benefits were affected.
Nearly twice as many people used the money to pay for daily living costs rather than pay off debts.
"The pension freedoms are popular with consumers but some people are experiencing unexpected losses," said Gillian Guy, chief executive of Citizens Advice.
"The changes are giving huge numbers of people the choice of how to access their retirement savings, offering them more options about how to use the money to best fit their lives.
"As people's pension choices become more complicated government and providers need to continue their work to promote free Pension Wise guidance, ensuring people are fully informed about their options as they move from work into retirement."
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The report also found that 29% of those who had withdrawn money put the funds into a bank account.
Steve Webb was the pensions minister when the system was announced and is now director of policy at Royal London pensions company.
"If pension savers are putting their money into a bank account on a temporary basis before reinvesting it, then there is less to worry about.  But if they simply leave their money in an account paying little or no interest, they will see its real value decline year-after-year through inflation," he said.
"It is vital that anyone considering taking their money out of their pension pot has access to high quality advice and guidance, which stresses the option of leaving the money invested."
Earlier in the month, the Association of British Insurers - which represents many pension companies, said that a minority of those aged 55 and over were withdrawing too much from their pension pots.
Some people are being hit with an unexpected tax bill after unlocking their money from a pension pot, according to Citizens Advice.