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1a) He went through her phone and found out she'd been lying to him all the time.
1b) He went through her phone and found out she was lying to him all the time.
2a) My friend asked me to watch that film and made me realize what I'd been missing.
2b) My friend asked me to watch that film and made me realize what I was missing.
What's the difference here and what's more correct and natural?
The past perfect and past perfect continuous talk of a time before a past event. You can think of this as something happening in the past of the past, i.e. further back in time than the past, before the past if you like. When you say "I found out", this is in the simple past, therefore to talk about the time before you did that, you need to use a past perfect form "that she had been lying" or "she had lied", because the lying happened before you went through her phone.
Note that in informal speech you may hear some native English speakers ignore this rule. That doesn't mean it's correct though.
Note also that it would be better to use "all along" rather than "all the time". She had been lying all along. This is a common collocation. "All along" means "all the time, from the beginning".
"Went" and "asked" are each simple past tense, and they set the context for the rest of the sentence, which must be from the point of view of when the "went" or "asked" happened.
1b) He went through her phone and found out she was lying to him all the time.
So, from that perspective, "was lying" indicates something that is happening in the current time; she is lying right now. But the phone shows nothing about what is happening now, only in the past. These two tenses don't get along here, and this sentence thus sounds awkward.
1a) He went through her phone and found out she'd been lying to him all the time.
She had been lying in the past, not now, and that fits correctly with the given perspective.
The second example is almost the same, but not quite. "I had been missing" is correct for the same reason as above, but "I was missing" could also be correct, depending upon context:
a) … made me realize what I'd been missing. So we arranged to watch it next week.
This is like the first example.
The "*had been missing" is in the relative past, while the "missed" and "arranged are in the relative present. They fit together correctly.
b) … made me realize what I was missing. So we watched the film right away.
In case "b" though, "I was missing" is in the speaker's present. But that's okay here, because the "we watched is in the same tense as the "made me" and happens in the same time sequence.
One trick you can do is to reword the sentence into the perspective of the initial context:
1a) He goes through her phone and finds out she has been lying to him all the time.
1b) He goes through her phone and finds out she is lying to him all the time.
[The "is" is present tense, but he doesn't know she is lying right now. so this is wrong.]2a) My friend asks me to watch that film and makes me realize what I have been missing.
2b) My friend asks me to watch that film and makes me realize what I am missing, so we watch it right away.
1a) ... she had been lying all the time
This is past perfect continuous, which describes something that happened continuously before some event in the past, in this case she had been lying to him over a period of time before he went through her phone.
1b) ... she was lying all the time
This is past continuous which it usually describes what was going on at the time something else (going through her phone) happened. Adding "all the time" emphasises that it had been going on for a long time, and we can probably infer that this occurred before he went through the phone.
2a) is past perfect continuous, and indicates that the speaker had been missing something (presumably the pleasure of watching the film) up until their friend persuaded them to watch the film.
2b) is past perfect, which describes what was going on (they were missing something) around the time that they watched the film.
For something that a person had missed up until a particular event, past perfect continuous is formally correct, though as this NGram graph shows, in recent years, the phrase "what I was missing" has increasingly been used about something that was absent from somebody's life until a particular event.
Here is an example:
I didn't know what I was missing until I got the chance to be out on my own - Ajax's harpy holiday - Mychal Daniels 2016
