Cracking the knuckles is makrooh whilst praying

Cracking the knuckles is makrooh whilst
praying, not all the time. Rather it is makrooh during prayer, because it
will either distract the one who does it from the prayer, or it will disturb
other worshippers. 

The hadeeth that was narrated concerning
that is not the words of the Prophet (blessings and peace of Allah be upon
him); rather it is mawqoof and its isnaad ends with ‘Abdullah ibn ‘Abbaas
(may Allah be pleased with him) and is his words. 

It was narrated that Shu‘bah, the freed
slave of Ibn ‘Abbaas, said: I prayed beside Ibn ‘Abbaas and cracked my
knuckles, and when I had finished praying, he said: May you have no mother!
[This is a word of rebuke] You crack your knuckles whilst you are praying?

Narrated by Ibn Abi Shaybah (2/344). Al-Albaani
said in Irwa’ al-Ghaleel (2/99): Its isnaad is hasan. 

Shaykh Ibn ‘Uthaymeen (may Allah have
mercy on him) was asked: Does cracking the knuckles absentmindedly whilst
praying invalidate the prayer? He replied: Cracking the knuckles does not
invalidate the prayer, but cracking the knuckles is a kind of fidgeting, and
if that is during a congregational prayer, it will inevitably disturb those
who hear it, and that is more bothersome than if there is no one around him.

End quote from Fataawa Arkaan al-Islam
(p. 341) 

The Standing Committee for Issuing Fatwas
was asked (fatwa no. 21349): The Prophet (blessings and peace of Allah be
upon him) forbade interlacing the fingers in the mosque; does that include
cracking the knuckles? Please note that there is no hadeeth which forbids
it. 

They replied: A number of the scholars
stated that cracking the knuckles is makrooh inside the mosque, and they
connected it to interlacing the fingers, because both come under the heading
of fidgeting.

End quote from Fataawa al-Lajnah ad-Daa’imah
– 2 (5/266) 

See also the answer to question no.
36801

And Allah knows best.