Brick Roof flashing question

We had to replace the counter flashing which went over the flashing between a brick wall and roof below the wall. THink of it as flashing a chimney and replacing the counterflashing where th chimney connects to the roof do to brick work on the chimney. A roofer was hired to install the counter flashing. He used a piece of counter flashing at each brick and stepped it to follow the slant of the roof and overlapped with the next piece of counter flashing. He ground it into the mortar joint and sealed it with some type of cement. My question is whether the verticle joints between the pieces of counter flashing should be sealed with caulk or cement. Seems to me they should be but he left them open. They overlap but are not sealed in any way. Thanks.