Msp22 Spary

Hi.i have paid in to an stocks and shares isa's for the past 4 years,one which was set up in 2004 of which I pay 200 per month and the other has some shares which I moved into the other isa to protect from capital gains.i realised this mistake this week and have contacted the second isa provider about this.why has this mistake been missed by hrmc and the provider for so long? I know its my responsibility but surely there needs to be better safeguards. I don't know what to do.the shares when bedding to an isa was within the cgt limits in each of the tax years.