I recently saw a video done by a self-proclaimed non-filmmaker mom. Overall, the video was amazing. However, at one point there was something odd as her image faded down. I have recreated the effect in the video below.
Within video if you fade two stacked layers at the same time, the top one will show through to the bottom layer, giving a very odd feel to the transition. To compensate for this, you must first flatten the image so that the single layer fades cleanly.
Multi-Layer vs. Single Layer
Keep that in mind as you work on your productions. If something looks wrong with a multi-layer transition, flatten the images/video/text to one track and try the transition again.
Your Media Production Mentor