There is some bad blood between Lesnar and WWE. It all began pretty much at the beginning of Lesnar's career. Jim Ross (who was head of talent at the time) signed Lesnar to a development contract after being impressed with Lesnar's legitimate athleticism and accomplishments in amateur wrestling. Lesnar trained at OVW and Vince McMahon fell in love with him. Lesnar had the body, the size and the look along with the wrestling ability and similar athletic background of Kurt Angle.
In 2002 Lesnar was called up to the main roster, he was paired with Paul Heyman (Vince put his personal feelings with Heyman aside here because he knew Heyman could get Lesnar over) and given the biggest initial push in WWE history. In April he debuted and destroyed Matt and Jeff Hardy in a feud that lasted a little over a few weeks. In June he dominated and defeated Hulk Hogan before going on to win the King Of The Ring Tournament. In August he defeated The Rock to win the WWE Championship in the main event of Summerslam.
By 2003, Lesnar was the top guy on Smackdown and one of the top guys overall in the WWE (behind only Triple H and The Undertaker). He won the 2003 Royal Rumble and went on to defeat Kurt Angle in the main event of Wrestlemania for the WWE Championship.
To put this into perspective, in Lesnar's first year with the WWE he was booked clean over pretty much everyone (including Hogan, Rock and Undertaker), won the King Of The Ring, headlined Summerslam and won the WWE Championship, won the Royal Rumble and then won the WWE Championship for the 2nd time in the main event of his first Wrestlemania. From the get go, Brock was destined to be Vince McMahon's biggest star but...It started to go wrong.
Following Lesnar losing the title to Kurt Angle and then regaining it, Brock turned heel. Following a series of feuds that didn't really amount to much, Brock lost the title to Eddie Guerrero and it was decided he and Goldberg would meet at Wrestlemania. It's been rumored that the long term plan was to have Brock feud with The Undertaker outside of the WWE Championship picture and they wanted Brock to lose a series of times to Taker. According to some people, Brock didn't like this percieved demotion.
Shortly before Wrestlemania, Lesnar negotiated himself out of his contract in order to pursue his dream of playing American Football. This likely caused a lot of bad blood between Vince and Brock because it was expected that Brock would stay long term. One of the clauses attached to Lesnar's release, was that he could not work for any professional wrestling or mixed martial arts organisation until June 2010. With his release secured, Lesnar left WWE after losing to the also departing Goldberg at Wrestlemania 20.
Brock Lesnar failed to make the NFL cut and when he failed to find work in any other athletic avenues, he decided to contest the no compete clause. WWE were extremely pissed and filed a countersuit that protested Lesnar appearing in a non-wrestling role in NJPW. The case nonetheless was dropped and WWE negotiated a new contract for Lesnar to return. Ultimately these negotiations fell through and the original case was ruled in Lesnar's favour, making him free to return to other pro wrestling organisations.
In 2006 he joined NJPW, where he was pushed strong and won the IWGP World Heavyweight Championship. Eventually he joined Antonio Inoki's IGF promotion and he was stripped of the IWGP World Heavyweight Championship. Nonetheless, Inoki disputed this decision by NJPW and presented Brock with the IWGP Third Belt Championship (which served as the IGF's title). Brock would go on to lose this to Kurt Angle who would then lose the title to IWGP Champion - Shinsuke Nakamura in a unification match.
Brock left the WWE on pretty bad terms. It's surprising that Vince McMahon has agreed to negotiate with him, but despite whatever bad blood may or may not remain, they appear for now to have put it all aside for business purposes.