Leveling Accusations against Allah
al‑Imam al‑Sadiq (as) said: "Whosoever seeks the best from Allah in his affair, and acts upon one of the options (either performs or does not perform an action) but has something enter into his heart (unhappiness or doubt regarding to how he acted), has leveled an (unfounded) accusation against Allah." 
It is possible that not being truly happy with the outcome of the Istikhara has it roots in one of the following:
1. Doubt whether Allah (swt) truly wants the best (for His servants), which in reality is laying an unsupported accusation that Allah is greedy and does not want good for His servants.
2. Doubt in the knowledge of Allah concerning what is truly good, which in reality is laying the charge that Allah is ignorant and is imperfect.
3. Doubt in the power of Allah in deciding what is truly the best. This action charges Allah with being weak and powerless.
4. Doubt that Allah (swt) does not pay attention to His servants and their asking for the best from Him. This action insinuates that there is some defect in the mercy of Allah .
One must have complete certainty in whatever Allah has decided, and be pleased that He would do only what is good for His servants. This is because without a doubt, Allah will guide His servants to that which is good and that in which lies his betterment, however many sins the servant of Allah has on his record.
Being Distanced from the Mercy of Allah
al‑Imam al‑Sadiq (as) was once asked: "Who is the worst creation in the eyes of Allah?" The Imam r6,replied, "The one who levels an accusation against Him (Allah). " The person retorted, "Is it possible for a person to level an accusation against Allah?" The Imam (as) ,replied, "Yes. The one who asks Allah for the best and it (the best) is given to him but in the way of something that he does not like, and he becomes upset. Thus, this is the one who has leveled an accusation against Allah. ‘’ 
 Bihar al‑Anwar, Volume 91, Page 225
 Makarim al‑Akhlaq / Mahasin Barqi, Page 598, Hadith 5 / Bihar al‑Anwar, Volume 91, Page 223, Hadith 2