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Too many uncalibrated images from phantom 2 V+

We are trying to map a trail that is 20 m wide and 4km long with our DJI phantom 2 V+. 

We fly the site in Pix4d’s manual mode to take pictures every 15m and it works very well. However, when we try and process the missions, we are getting very weird outputs. The orthomosaic is either shifted or missing pieces, the model is slanted or missing pieces. 

 

We reviewed the images and they have great overlap with clear resolution. 

 

Could someone help me out as to why 100 / 324 images can become uncalibrated? 

Adding MCP will help the software, better is to also add GPC reference points.