Thank you for the additional information about your problem. This is likely due to the fact that your automated mission was piloted in fast mode. When your drone is flying a mission in fast mode Pix4Dcapture will tell your drone when to take a picture as it progresses through the automated mission. If there is a drop/interference in the communication between your drone and Pix4Dcapture, the signal of when to take a picture may not be received. When this communication is interrupted you are sometimes left with missing images and a lack of overlap.
We do not expect this problem to occur regularly, as our team has found it difficult to reproduce. This problem has been discussed to a reasonable extent in the thread HERE. I encourage you to read over what other users have discussed and suggested as our team continues to look into this problem.
@Audrone
Thank you for joining in on the conversation. Missing photos is not a common occurrence when utilizing “Safe Mode”, as this mode works differently than safe mode. I would like to discuss this further via an official support ticket. I will post the results/conclusion of the support ticket in this thread so other users can reference it.