So after a day of flying Spark I notice that not all the files are transferred to the phone (iPhone 6) but they are on the SD card. What may cause this? Why is there missing clips between SD card and phone?

Hi, Filip. I would recommend you connect your spark with your phone and tap playback in the image screen. You can choose the cache files and save them to your phones.

There is a limit on the cache size.  If you hit that limit, I believe it will delete the oldest file.  

I think the limit is 2gb.

Keep in mind the cached version is low resolution, so only use the cached version if you want to see what you did.  I wouldn't use them to store or edit off.  Get them off the card or download them from the Playback menu