Aiken, a southpaw pitcher who attended San Diego High School prior to being drafted, originally agreed to terms with the Astros on a $6.5 million signing bonus.
However, Houston decided to lower the signing bonus offer following x-rays and concerns over the lefty's elbow.
According to reports on ESPN.com, the head of the players' association says the union is working with Aiken and the pitcher's advisers to explore “all legal options.”
Due to Houston's failure to reach terms with Aiken, the Astros were also unable to sign fifth-round pick Jacob Nix.
Nix also attended San Diego High School and is a personal friend of Aiken's.
"Today, two young men should be one step closer to realizing their dreams of becoming Major League ballplayers," union head Tony Clark said in a statement. "Because of the actions of the Houston Astros, they are not. The MLBPA [Major League Baseball Players Association], the players and their advisers are exploring all legal options."
The Astros also issued a statement regarding the team's failure to sign Aiken, claiming that Houston's final offer to the southpaw "was extremely fair considering all the factors involved in this case."
Although the MLBPA is trying to call a balk on the Astros, Houston insists the team was only looking out for the best interest of all parties involved when they attempted to renegotiate a deal with Aiken.
"As always, we approached these negotiations in good faith and with the best interests of the Astros organization in mind, both short-term and long-term," the team said, according to ESPN.com. "Throughout this entire process, we have absolutely acted within Major League Baseball's rules and guidelines, which MLB has confirmed on numerous occasions."
Aiken was the first left-handed pitcher to be drafted in the first five picks since Adam Loewen (fourth overall to Baltimore in 2002).
Both Aiken and Nix are committed to UCLA next season, and both players are also being advised by Casey Close.
Numerous scouting reports list Aiken throwing fastballs that hit 96-97 mph, along with a solid curve ball and a tough changeup.
"It's the most advanced high school pitcher I've ever seen in my entire career,” Astros general manger Jeff Luhnow said. "He has command like I've never seen before of his stuff.”
Surrounded by controversy and possible future lawsuits, the consensus No. 1 pick in the 2014 MLB Draft will now be available for baseball's 2015 draft.
Only time will tell if Houston made the right decision by failing to sign both Aiken and Nix.
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Denton Ramsey may be reached via email at TXSWReport@gmail.com