For the left picture if I click the text, it goes right to its place but with all of these tables, I can’t be checking everything all the time and it’s an important work, so I want the PDF to look as it’s supposed to.
This doesn’t happen with the right picture though
Here’s a couple of screenshots (the black rectangle is a page break)
Here’s a sample: sample.odt
OS: GNU/Linux Manjaro 20.0.3
DE: KDE 5.70.0 / Plasma 5.18.5
LibreOffice 6.4.4.2 40(Build:2)
The same in Version: 6.3.6.2 (x86); Build ID: 2196df99b074d8a661f4036fca8fa0cbfa33a497; CPU threads: 4; OS: Windows 6.1; UI render: default; VCL: win.
“appears this way” ?? This is not self-explanatory. Please edit your question to describe the difference with words.
First/second picture? Do you mean left/right picture? They seem to cover different situations.
They easiest way to diagnose is to attach a 2-3 page sample (put the 2 tables; don’t worry for page limits, I’ll add text before the table to cause a page break inside the table).
You’re absolutely right. I’ve just edited the post
Your tables have a “complex” structure: cells in the first column are merged as their contents are common to several rows in the other columns. All cells have content vertically centered.
In Table>Properties, we see that the tables can split across several pages (necessary because the tables span several pages) and rows can also split.
This is usually fine, but here the merged cells in the first column introduce a disturbance. When a page break cause a row split, Writer gets confused about how spread first column text. It seems to compute correctly the amount of text is the split parts of the cell but is lost when it comes to position the text: top or centered in the part before the break and seemingly full centering space in the part after the break as if the cell has not been split with the result of clipping overflow text.
It is a bug. Please report it on bugs.libreoffice.org and attach this sample as an example.
Meanwhile, some workarounds may mitigate this bug (without curing it totally):
Another way to fix the problem would be to change a bit the look of the table.
Instead of merging vertically, you merge horizontally one row across the width of the table. In this wide cell, you enter your “Bloques y suspesos” or “CE” aligned on left or centered (to your taste). The “CE y CC” or “EAE” remain in their second column with the first column still merged to show the extent of the applicable rule but it is empty, thus not causing Writer confusion.
I also suggest you use built-in character style Vertical Numbering Symbols when you want text written vertically instead of your present manual formatting. It will be easier to manage centrally.
Also, use a multi-level list for numbering your items: level 1 in first column, level 2 in second column (just type a tab character at start of item to promote it at level 2; this “level tab” does not show up on print). This is more reliable and allows you to add, reorder or delete items without caring for the numbering: the are automatically renumbered.
EDIT
See in Tables.odt a proof of concept about the change in table presentation and use of list numbering. Note I did not pay attention to details of formatting (font face, size; …). I used two paragraph styles for the list because your numbering is different in the tables: in the first you only have one number in the current level, while in the second you display the full number hierarchy.
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Thank you very much for your complete answer! 
As you suggested, I’ve just submitted the bug
About changing the style: it’s kind of the style I’m asked for so I can’t change much tbh, but thank you so much for the recommendation!
About numbering: I know haha but it’s a copy/paste of an official document, so using vertical numbers would take more space and take more time, but thank you so much again! 
If the page limit allows me to include the header I probably would do it, because it’s much better this way!
For the record: link to bug report in preceding comment is tdf#133946
