FSCS confirmed it was carrying out an investigation after its communications could have led clients to believe their investments with the ill-fated firm were protected when they were not.
LCF slumped into administration in January with 14,000 bondholders with holdings totalling £236m.
Since then, in March, the Serious Fraud Office revealed there had been four arrests in connection with LCF's collapse.
An FSCS spokeswoman said: “We have been made aware of a small number of communications from FSCS which may have given a partial picture and we are seeking to establish the number and nature of their content.
“While it is true to state that FSCS protection would cover regulated activities carried out by LCF, we accept these efforts to inform people may have led to confusion about the extent to which our protection extends to these particular mini-bonds.
“As part of our investigation we will examine each of the individual cases and respond to them directly.
“We are sorry for the confusion this may have caused some LCF customers.”