@Ikael: I found a couple of issues. Just after posting, of course.

Issue 1
On an NPC sheet, drop the Small hindrance.
Drag NPC into CT.
Size in CT is set to -2, but -1 is expected, as per the hindrance description. It appears the "Small" keyword supersedes the effect [Size -1].
The Small hindrance keeps the effect in the description, unlike on the PC sheet, where it adjusts the stats and drops the effect. So you see -1 on the npc, but -2 in CT.
You can change the hindrance name to "Very Small" and drop the npc into CT and see the size set to -3 (or to -4 for Tiny) and ignore the effect when setting the Size field. So the keywords are working properly.
This is confusing in that when creating an npcharacter (vs monster), you'd use hindrances rather than racial abilities, so you'd pick the Small hindrance rather than the Size ability. In that case it seems to not work properly.
Attacks against the NPC are calculated as Very Small, because it combines the keyword Small and effect [Size -1]. This makes it seem to calculate the effect improperly, if you don't know about size keywords.
Since this is a hindrance that uses an effect, should it behave like the PC sheet and use the effect instead of size keyword?

If you add a [Size -3] to this npc, it will now stop calculating size mods on attacks. This happens if you add it to the effects line in CT or to the character.
This could happen with the effect from the Shrink power, for instance. I would expect the max size penalty to apply.


Issue 2
A second issue, this one with setting size. Maybe a bug?
Drop the Size ability onto an npc sheet. Use the effect to set specific size, but don't rename the description. e.g.
Code:
Size
    [Size -2]
Drop the npc into CT. The size field remains blank.
Attack the npc; the size calculates properly, even though size doesn't show in CT. Not exactly an error, but it could cause confusion. (This isn't the bug.)
Open the npc from CT, adjust the size effect e.g. [Size -6], and it now does not calculate size at all.
The issue is that Size -6 is invalid, so size calculate is circumvented.
Should this instead check against > max size and set to max size? The player won't know there's a ceiling, but it will still "work".

Related points:
Set [Size -2], as above.
Add a second [Size -4] effect.
Again, size adjustments are ignored. Two lines with [Size -2] works, but the total exceeds max size and skips size calculations.

Add Size ability, set to [Size -4]
Add Small hindrance.
Attacks against the npc don't calculate size, because total exceeds max.


Issue 3
I'm not sure this is a bug, because it's understandable what's happening if you understand FG. But it can be confusing to others.
Drop the Size special ability onto an npc.
Change "Size" to "Small"
Add effect [Size -2] under Small.
Drop npc into CT.
Size field is set to -2, as expected, due to size keyword.
Attacks against npc calculate as Tiny.
Open npc from CT, delete effect.
Attacks now calculate as Small.
Open npc from CT, add effect [Size -1]
Attacks against npc calculate as very small.
In this case, the size keyword (or size field in CT) is combining with the effect. It's a matter of knowing to use either keywords or size effects, not both at once. And changing the size in CT appropriately.
Is it possible to update the Size field in CT, and combine size keywords with effects? That may still be confusing if you don't know about size keywords. Maybe totaling keywords and effects would be enough clue? I don't know what would help in this case.

Issue 4
I'm not sure this is a bug, per se. It's a matter of CT not changing the size field when npc character sheet is updated.
Add size to npc, change "Size" to "Very Small". Don't add size effect.
Drop npc to CT. Size sets to -3, as expected.
Attack npc to verify attacks calculate size penalty properly.
Open npc from CT. Change "Very Small" to "Small"
Size in CT does not change.
Attacks against npc still count as Very Small (it honors size field in CT over keyword)
CT doesn't update size field, which could be an expected event and a point of confusion.
Could you add an event handler to catch this change and update size in CT, like is done with the PC sheet?

I still can't recreate the original bug. I was able to when it was posted, but can't now. Next time I'll post the details to recreate it right away.