its not confusing. it shows its that Soundwave (and every decepticon that knew of earth) left earth around the 70s, but in a ship very slow. thus didnt made it to the nemesis till the 90s, but when they realized megatron was in Earth they made to mars in 2007 and then to earth, but it was too late, Megatron was dead. (And every con that joined soundwave were left in stasis on the moon)

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I would have to say the Soundwave back story will Dillon and his father bother me.

The plot for the first movie was for the Autobots to have finally made it to earth with the Decepticons already here searching for Megatron. The story in DOTM claims that Decepticons have known about Earth (possibly a long time since Sentinel was supposed to meet up with Megatron) for sometime and have been meddling in its affairs.

This means Soundwave has been on Earth for a few decades and was either not looking for Megatron or was still following a plan to pillage Earth that Megatron came up with before he crash landed.

DOTM also negates the story of the Fallen. Megatron was to be serving him and searching for the cube to destroy Earth's sun and harvest its energy. Destroying the planet. All of Soundwaves plans and meddling were for nothing. Megatron didn't seem like he wanted to overthrow the Fallen and then take Earth over.

For me, its not each movies plot that is troublesome. Its the overall story of the 3 that make no sense.
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Look at this, it wil lhelp you will all those plot hole
Movie timeline - Transformers Wiki