High value transaction in saving bank account

I am one of the director of a company, I have 3 saving bank account, iam getting 2lac as salary, but in my saving bank account some transactions ( some bill payments of below 10000 and ATM withdrawals) have done for company purpose. all aggregating around 5-8 lacs from 01-04-2016 - 31-10-2016. ( 5-8 lac amount deposited as multiples of small amount like 40000,10000, 25000 etc )   I am not a income tax payer but i do file return with zero income tax by showing total income below 2.5lacs, also am not keeping balance above 50000 in any of my saving account. should i face any issues from income tax department?