The verse in Qur'an 2:29 that you quoted says:
هُوَ الَّذِي خَلَقَ لَكُم مَّا فِي الْأَرْضِ جَمِيعًا ثُمَّ اسْتَوَىٰ إِلَى السَّمَاءِ فَسَوَّاهُنَّ سَبْعَ سَمَاوَاتٍ ۚ وَهُوَ بِكُلِّ شَيْءٍ عَلِيمٌ
It is He who created for you all of that which is on the earth. Then He directed Himself to the heaven, [His being above all creation], and made them seven heavens, and He is Knowing of all things.
— Surat Al-Baqarah 2:29
The verse is talking about:
- Creating "all of that which is on the earth" (خَلَقَ لَكُم مَّا فِي الْأَرْضِ جَمِيعًا), i.e., rivers, mountains, etc., not creating the Earth itself (already created).
- Allah directing Himself to the heaven (اسْتَوَىٰ إِلَى السَّمَاءِ) in a singular form (already created), which He then turned it into seven skies (فَسَوَّاهُنَّ سَبْعَ سَمَاوَاتٍ) in the plural form.
There is no chronological order in this verse.
The verse you may be questioning is Qur'an 21:30 in which Allah ﷻ says that the seven skies and the Earth and what is in between was all in one piece at the time before they were separated:
أَوَلَمْ يَرَ الَّذِينَ كَفَرُوا أَنَّ السَّمَاوَاتِ وَالْأَرْضَ كَانَتَا رَتْقًا فَفَتَقْنَاهُمَا ۖ وَجَعَلْنَا مِنَ الْمَاءِ كُلَّ شَيْءٍ حَيٍّ ۖ أَفَلَا يُؤْمِنُونَ
Have those who disbelieved not considered that the heavens and the earth were a joined entity, and We separated them and made from water every living thing? Then will they not believe?
— Surat Al-Anbya 21:30
Another verse that clearly shows that the Earth was created first is Qur'an 41:11, where Allah ﷻ tells us that the sky (single sky) was in smoke form and attached to the Earth, then Allah commanded them to go to Him:
ثُمَّ اسْتَوَىٰ إِلَى السَّمَاءِ وَهِيَ دُخَانٌ فَقَالَ لَهَا وَلِلْأَرْضِ ائْتِيَا طَوْعًا أَوْ كَرْهًا قَالَتَا أَتَيْنَا طَائِعِينَ
Then He directed Himself to the heaven while it was smoke and said to it and to the earth, "Come [into being], willingly or by compulsion." They said, "We have come willingly."
— Surat Fussilat 41:11
In Qur'an 41:11, we see the Earth itself as a structure was created, and there was one sky in a smoke form attached to it. Qur'an 2:29 shows that what is on the Earth was created then the single sky was split into seven skies. Qur'an 21:30 shows that the skies and the Earth (and what is in between) were separated.
Note. You may refer to the answer to your question on the use of the different words for sky, skies, and that the word may be used to include what is in between, too.
Although I do not see the contradiction
In the tafsīr of 41:11, Ibn Kathīr said that the smoke coming out that formed the sky was a result of very high temperatures that caused waters to evaporate. This could very well be a reference to primordial singularity all the way until structure formation.
Almost a century ago, Slipher assumed that all spiral galaxies receded from Earth. Then Friedmann hypothesized that the universe might be expanding. A good portion of scientists, however, were concerned that the Big Bang Theory seemed to confirm religious concepts, especially that Lemaître, who was a Roman Catholic priest, concurred that the world started as a single quantum and is in expansion state. They preferred a steady-state model to keep physics "unreligious". However, observations by Hubble seemed to confirm the theory that the universe was expanding as Hoyle said a few decades later. The Big Bang theory is still forming until today, and the "small scale crisis" has a huge room for improvement.
Islam SE is a forum about Islam. So, the basis is Islam. If the Big Bang theory does not agree with the Qur'an or the hadith, then the Big Bang theory is "un-Islamic", rather than the verse in the Qur'an being "unscientific".