I think that you have confused the binding energy of a nucleus with the Q-value of a nuclear reaction both of which are found using the relationship $E=\Delta m \, c^2$.
The mass defect of a nucleus is equal to the sum of the individual masses of all the particles which make up the nucleus minus the mass of the whole nucleus and it is a positive quantity.
Multiplying the mass defect by the speed of light squared gives you the binding energy of a nucleus - the energy required to split up a nucleus into its constituent parts.
In reaction we use this formula to calculate binding energy of that reaction.
If there is a reaction of the form $A+B \rightarrow C+D$ then the change in mass is
$ (m_A+m_B) - (m_C+m_D)$
and the Q-value of the reaction is given by the equation
$Q=[ (m_A+m_B) - (m_C+m_D)] \, c^2$.
In such an example the value of $\Delta m$ and hence $Q$ can be either positive or negative and you will often see the equation for the reaction written as $A+B \rightarrow C+D+Q$.