The "scientific miracles" that some preachers have propagated such as embryology, invisible barriers between seas, earth being round, moonlight being reflected, iron being sent from space and the deep ocean being in darkness etc. are modern, out-of context and willful interpretations and not an established part of Islamic teachings, nor have the Muslims traditionally used these 'miracles' to give dawah. Some of these, for example the oceans being dark, were assumed to be common knowledge and that was the reason God gave it as a parallel.
The Quran wasn't sent as a textbook to teach science, nor was it sent as a technical documentation on the universe, nor were its observations given from human perception or physical eyes, nor was it directed at people who were to come 1400 years later.
The purpose of the Quran was to guide the moral and spiritual lives of the people ... especially the people of Arabia in antiquity. Its miracle was in its Prophecy and the mystical effect of its verses ... the Sahabah embraced Islam because when they heard the verses it evoked something deep in their hearts and they were inspired by it (the reason the Kuffar called it sorcery) ... they didn't pick up a microscope and started dissecting fetuses.
1- quran says that, the flesh of the embryo is formed after the bones, while some scientists claim it to be an error and false, they form at the same time
The actual Quranic verse is:
Quran 23:12-14 And certainly did We create man from an extract of
clay. Then We placed him as a sperm-drop in a firm lodging. Then We
made the sperm-drop into a clinging clot, and We made the clot into a
lump [of flesh], and We made [from] the lump, bones, and We covered (lit. clothed)
the bones with flesh; then We developed him into another creation. So
blessed is Allah, the best of creators.
The Quran says that the muḍ'ghata (lump of flesh) comes before the bones are formed, and that the bones are clothed with flesh (the word used is kasuna instead of khalaka [created]).
Quran 22:5 O People, if you should be in doubt about the
Resurrection, then [consider that] indeed, We created you from dust,
then from a sperm-drop, then from a clinging clot, and then from a
lump of flesh, formed and unformed - that We may show you. And We
settle in the wombs whom We will for a specified term, then We bring
you out as a child, and then [We develop you] that you may reach your
[time of] maturity. And among you is he who is taken in [early] death,
and among you is he who is returned to the most decrepit [old] age so
that he knows, after [once having] knowledge, nothing. And you see the
earth barren, but when We send down upon it rain, it quivers and
swells and grows [something] of every beautiful kind.
The interpretation given in Tafsir Ibn Kathir:
(then We made the clot into a little lump of flesh,) which is like a
piece of flesh with no shape or features.
(then We made out of that little lump of flesh bones,) meaning, `We
gave it shape, with a head, two arms and two legs, with its bones,
nerves and veins.'
(then We clothed the bones with flesh,) meaning, `We gave it something
to cover it and strengthen it.'
(and then We brought it forth as another creation.) means, `then We
breathed the soul into it, and it moved and became a new creature, one
that could hear, see, understand and move.
Bear in mind that the purpose of the Quran is to describe the creation in a poetic manner to illiterate people in late antiquity, and not to give a technical details like a book on biology, nor to publish a research paper in the International Journal of Biological sciences.
2- quran says that the moon reflects the suns light while atheist and islam haters say that it was discovered already years before islam by an ancient greek philosopher
The Quran doesn't explicitly state that the moon reflects light. Preachers derive this from the fact that the sun and stars are called "lamps" in the Quran while moon is not. They also argue that nur always means reflected light, which isn't something that I've ever found in any tafsir or arabic dictionary.
3- quran says the there are two seas whi meet but don't mix, while it has been discovered that they eventually meet.
The verses of the Quran are:
Quran 55:19-21 He released the two seas, meeting [side by side];
Between them is a barrier [so] neither of them transgresses. So which
of the favors of your Lord would you deny?
Quran 25:53 And it is He who has released [simultaneously] the
two seas, one fresh and sweet and one salty and bitter, and He placed
between them a barrier and prohibiting partition.
The two seas mean fresh water, for example rivers, lakes, springs etc. and sea water, though there are also interpretations that this means clouds\rainwater and the water on the earth. The partition between them is usually understood to mean the dry land separating them. The partition prevents them from mixing, as in contaminating the fresh-water ... and its common sense that one could fill-up a basket of fresh-water and pour it in the sea ... and its common sense that evaporation and rain etc. would cause molecules to mix ... the point is that the body of freshwater is not salinated and the sea water is not purified by their mixing.
From Tafsir Ibn Kathir:
(meeting together.) Ibn Zayd said, "He prevents them from meeting by
the dividing barrier He placed between them to separate them.'' The
two seas are the fresh and salty waters, the former coming from
running rivers. We discussed this topic in Surat Al-Furqan when
explaining Allah's statement;
(And it is He Who has let free the two seas: one palatable and sweet,
and the other salty and bitter; and He has set a barrier and a
complete partition between them.)(25:53) Allah said,
(Between them is a barrier which none of them can transgress.)
meaning, He has placed a barrier of land between these two types of
waters, so that they do not transgress upon each other, which would
spoil the characteristics they were created with.