All perfect praise be to Allah
Some of the Sahaabah complained about the waswaas that was bothering
them. Some of the companions of the Messenger of Allaah (peace and
blessings of Allaah be upon him) came to the Prophet (peace and
blessings of Allaah be upon him) and said to him, ‘We find in
ourselves thoughts that are too terrible to speak of.’ He said, ‘Are
you really having such thoughts?’ They said, ‘Yes.’ He said, ‘That is
a clear sign of faith.’”(Narrated by Muslim, 132).
Al-Nawawi said in his commentary on this hadeeth (narration): “The
Prophet’s words, ‘That is a clear sign of faith’ means, the fact that
think of this waswaas as something terrible is a clear sign of faith,
for if you dare not utter it and you are so afraid of it and of
speaking of it, let alone believing it, this is the sign of one who
has achieved perfect faith and who is free of doubt.” from here
So, according to the situation you have described, if the person's thought is that oh i can't understand this things, this seems like such and such which is not possible, let me search about it and clear my doubts than thats ok, thats the faith above hadees is talking about.
It was narrated from Ibn ‘Abbas (may Allah be pleased with them both)
that a man came to the Prophet (peace and blessings of Allah be upon
him) and said, “I think thoughts to myself, which I would rather be
burnt to a cinder than speak of them.” The Prophet (peace and
blessings of Allah be upon him) said, “Praise be to Allah, Who has
reduced all his [the Shaytan’s] plots to mere whispers.” (Abu Dawood).
So, such whispers has no effect.
But, if after finding any confusion in Quran, person thinks like, oh, this is impossible that a true religion and a true God will say anything like this, i think islam is not true religon (nauzubillah) or any such thing, then this is different. In a sense that muslim is not supposed to think like that, he must research about it, find the truth about it and its explanation. But not to doubt Allah or his words immediately.
The Prophet (peace and blessings of Allah be upon him) said, “Allah
will forgive my ummah (followers) for any insinuating whispers that
may cross their minds, so long as they do not act upon it or speak of
it.” (Agreed upon- BUkhari/Muslim)
So, this is also not a very big problem, just a little change of thinking is required. Because this kind of thoughts are forgiven by Allah according to all above ahadees.
I will also like to quote:
Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him) said in Kitab al-Eeman: “The believer may suffer from the whispers of the
Shaytan insinuating thoughts of kufr (disbelief), which may make him
feel distressed. The Sahabah (may Allah be pleased with them) said, ‘O
Messenger of Allah, some of us think thoughts which we would rather
fall from heaven to earth than speak of them.’ He said, ‘That is a
clear sign of faith.’ According to one report, ‘… thoughts which are
too terrible to speak of.’ He said, ‘Praise be to Allah, Who has
reduced all his [the Shaytan’s] plots to mere whispers,’ meaning that
the fact that these whispers come, but they are so greatly disliked,
and they are pushed away from the heart, is a clear sign of faith.
This is like the mujahid (warrior) to whom the enemy comes, but he
resists him until he overwhelms him, and this is a mighty jihad
(battle)… Hence the seekers of knowledge and devoted worshippers
experience waswas and doubts which others do not face, because they
(the others) are not following the way prescribed by Allah, rather
they are following their own whims and desires and neglecting to
remember their Lord. This is what the Shaytan wants, in contrast to
those who are striving to draw closer to their Lord by seeking
knowledge and worshipping Him. He is their enemy and seeks to prevent
them from drawing closer to Allah.” (p.147 of the Indian edition)
from Suffering From Waswas (Insinuating Whispers) of the Shaytan
But, if someone thinks he had severe waswasa from shaitan and he had his heart convinced for that waswasa for even some seconds, he should repent to Allah, make taubah, ask Allah to protect him from such wasawas, and better to repeat shahadah with his pure heart. Repeating shahadah is just to ensure his imaan, otherwise no one is declaring him kafir. He had a bad thought, and then it is clear. So its ok, but repeating shahadah will be still better, saying shahadah again and again is also a zikar which enhances imaan.
Allah knows best