A lot of the issues can be fixed by editing libraries/icons.xml

Add those lines:
<replace sel="/icons/icon[@name='ship_m_gunboat_01']">
<icon name="ship_m_gunboat_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_m_bomber.tga" height="128" width="128"></icon>
</replace>
<replace sel="/icons/icon[@name='ship_m_frigate_01']">
<icon name="ship_m_frigate_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_m_fight_01.tga" height="128" width="128"></icon>
</replace>
<replace sel="/icons/icon[@name='ship_xl_battleship_01']">
<icon name="ship_xl_battleship_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_xl_battleship.tga" height="140" width="140"></icon>
</replace>
<replace sel="/icons/icon[@name='ship_l_carrier_01']">
<icon name="ship_l_carrier_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_xl_fight_01.tga" height="140" width="140"></icon>
</replace>
<replace sel="/icons/icon[@name='ship_s_heavyfighter_01']">
<icon name="ship_s_heavyfighter_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_s_heavyfighter.tga" height="100" width="100"></icon>
</replace>
<replace sel="/icons/icon[@name='ship_s_scout_01']">
<icon name="ship_s_scout_01" texture="extensions\vroicons_stable\assets\fx\gui\textures\shipicon\ship_s_scout.tga" height="120" width="100"></icon>
</replace>

(This puts the Bomber icon to be used for Gunboats, I think it looks very fitting... kinda looks like CAS planes irl)

Other Entities like VRO Akita for Terrans require editing macro for the unit example:
\extensions\vro\assets\units\size_l\macros\ship_lint_frigate_akita_macro.xml

the file looks like this:
<?xml version='1.0' encoding='utf-8'?>
<diff>
<replace sel="/macros/macro/properties/identification/@icon">ship_l_frigate</replace>
</diff>

This info should help you fix most of the issues.