Does the voluntary federal income tax withheld of $3980.40 on my SSA 1099 make the them question return, now the say I owe another $3981+326 interest?

on line 18 I reported $5841 but other report $1860 a difference of -$3981  which is a voluntary Federal income tax withheld thru social security. the cannot see this filing electronically.  They now say I now owe $3981
plus $326 interes.