We ran a EOM CC3 calculation to get two roots.
In timer.dat, the last column says that there were 69 calls to SIGMA ALL and 49 to sigmaCC3.
However, looking into output.dat, it says there were only 21 CCSD iterations, and 20 and 25 CC3 iterations, which does not not add up. What is the correct number? Are there some additional calls to sigma and sigmaCC3 somewhere?

Can you post your output.dat and timer.dat? There are multiple sigma calls in each iteration if you’re asking for more than one root, and the total number of sigma calls depends on whether a root has already converged.