I love both of those movies but I missed the rip offs.
When Clint and the Marines invade Grenada in Heartbreak Ridge they use a phone to call the Pentagon to order an airstrike against some Cubans. They need to dig up a credit card to make the international call. Transformers repeats this scene when they place the cell phone call and have to use a credit card to call the Pentagon to order the A-10/AC-130 strike.
In terms of Independence Day, the general concept of the US acquiring alien technology and building a underground secret base to attempt to reverse engineer the technology, a la Area 51 from ID and Hoover Dam in Transformers