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Philadelphia, PA (SportsNetwork.com) - While the rest of the baseball world was falling over themselves saying goodbye to Derek Jeter the past few days, an ugly situation was unfolding in Houston.

The Astros you remember had the No. 1 overall pick in this past June's Major League Baseball First-Year Player Draft. They chose San Diego prep left-hander Brady Aiken, who was considered the best high-school arm in the draft thanks to a fastball that touched 97 mph.

As talented as Aiken is, the bigger reason why the Astros leaned his way, rather than, say, North Carolina State southpaw Carlos Rodon, was the fact that they thought they could sign him for less than the $7,922,100 bonus slot allotted to the first overall pick.

By getting Aiken to come in under slot the Astros would be able to sign other players drafted later on, like fifth-round pick Jacob Nix, to a higher amount without going over their bonus allotment.

By all accounts the Astros and Aiken's advisor, Casey Close, had a wink-wink $6.5 million deal that was never finalized. By doing so, the team also agreed off-the-record to a $1.5 million deal with Nix, who is also advised by Close.

However, since then an issue has come up with Aiken's ulnar collateral ligament, the same one that eventually leads to Tommy John surgery.

Now the Astros aren't saying what the issue is, but they have said the exam has shown something and do not want to give him the original offer agreed upon.

"Brady has been seen by some of the most experienced and respected orthopedic arm specialists in the country, and all of those doctors have acknowledged that he's not injured and that he's ready to start his professional career," Aiken's advisor Casey Close told Fox Sports.

Some reports have stated that the Astros have dropped their offer to $5 million. And it just so happens that the $2.9 million they'd be saving is exactly the bonuses the team would then hand out to Nix and 21st-round pick Mac Marshall without having to be penalized with the loss of a future draft pick for going over the bonus pool.

Close has even suggested that the Astros' offer is now $3.1 million, the minimum necessary to ensure a compensation pick next year should the two sides fail to reach an agreement.

If that were to happen, the Astros would get the second pick in the 2015 draft.

It's hard not to side with Aiken here, especially since the Astros tried to lowball him just minutes before taking him with a $5 million offer. And the signing of players below slot is a practice that's been utilized by the Astros in the past.

Remember back in 2012 when it selected high school shortstop Carlos Correa? He received a $4.8 million bonus, when the pick was slotted for $7.2 million. Houston applied the money it saved on Correa to go over slot with a $2.5 million bonus to high school right-hander Lance McCullers Jr.

Close, as well as MLBPA head Tony Clark, are accusing the Astros of manipulating the draft.

Aiken could always go to UCLA and wait three more years to get drafted again. But who knows how far the Astros will take this. Could they try to hurt his eligibility the way the Philadelphia Phillies did with Ben Wetzler?

In February, reports came out that the Philadelphia told the NCAA that Wetzler, their 2013 fifth-round draft pick, had violated the no-agent rule after he was unable to work out a deal with them. Eventually, he was able to pitch for Oregon State and the Miami Marlins drafted him in the ninth round this past year.

Time is not on the Astros' side here. Friday at 5 p.m. ET, is the deadline to get Aiken under wraps. Aiken still, hopefully, has UCLA in his back pocket. He is only 17. He could walk away. Then again if there is an issue with that elbow and he does need Tommy John surgery at some point, who knows how much money he would be risking.

Then again, teams didn't seem to shy away from the once-dreaded surgery in this year's draft, as East Carolina stud righty Jeff Hoffman had the procedure during the year and was still chosen No. 9 by the Toronto Blue Jays.

Losing Aiken would just be another blow to an Astros organization that doesn't seem very deep at the moment. Yes George Springer is blasting home runs, but Correa fractured his fibula and is lost for the season, while 2013 first overall pick, righty Mark Appel, continues to struggle in the minors.

Appel recently had a cortisone shot in his wrist and is pitching to a 9.57 ERA at High Class A Lancaster.

Regardless of what happens with Aiken, this isn't exactly an ideal beginning. And who knows how much damage they have done for the future with potential picks.

Time is ticking, though.