Video not rotating using AVMutableVideoCompositionLayerInstruction

Try using trackVideo in the initializer for your layer Instruction so it will use the AVMutableCompositionTrack's trackID rather than the source asset's trackID

Update:

You only need one AVMutableVideoCompositionLayerInstruction, so declare it before the loop with the AVMutableCompositionTrack as the parameter. Then on each iteration of the loop, set the necessary properties of the layer instruction (transform, crop rect) for the current video asset you're working with. You're controlling how the video content in the composition track should be displayed at each insert time.

At the end, place the single layerInstruction in the instructions array, and use that in the video composition.

var layerInstruction = AVMutableVideoCompositionLayerInstruction(assetTrack: trackVideo)
for i in 0...(videos.count-1){
   //...your other code here

   layerInstruction.setTransform(assetTrack.preferredTransform, atTime: insertTime)
   layerInstruction.setCropRectangle(CGRectMake(0, 0, 300, 300), atTime: insertTime)
}

var instruction = AVMutableVideoCompositionInstruction();
instruction.timeRange = CMTimeRangeMake(kCMTimeZero, insertTime);

instruction.layerInstructions = NSArray(object: layerInstruction);
var mainCompositionInst = AVMutableVideoComposition()
mainCompositionInst.instructions = NSArray(object: instruction)