[Senna]

Analyze Weakness (Tested with the Staff of eye so it was level 12) does not apply bonus damage at all. 

Before

Code:

System: Debug: Total Power for Staff of Eyes / Staff of Eyes was 56.
System: Debug: Before Use Skill called. Prinny, Senna, Sub-Attack, 1
System: Debug: Attack type: /obj/skill/fe_attack/sub. attack_nums:
System: Debug: Total Power for Staff of Eyes / Staff of Eyes was 56.
Senna attacks Prinny with Staff of Eyes!
Prinny takes 57 Light physical damage.
System:
* Initial Damage: 57 Light Physical, flags: , sk: null, wep: Staff of Eyes / /obj/items/equip/weapon/spears/staff_of_eyes
* play_atk_anim was 1.
* 0 Evade VS 238 Hit.  (Damage Hit Mod was 0)
*2 Roll(s) Remaining. This one was a hit.
*1 Roll(s) Remaining. This one was a hit.
* Critical check: 47 Critical VS 0 Critical Evade. (57)
* armor was allowed. armor_reduc was 0. (57)
* spec_flat_reduc was 0. (57)
* amp_multi was 1. (57)
* reduc_multi was 100. (57);  MAG DEF, 0 PHYS DEF, 100 REDUC
* elem_reduc was 0. (57)
* Damage caps applied. (57)
* Damage shields applied. (57)
* Final damage was: 57.
System: * basic_attack(atk:Senna,def:Prinny,W:Staff of Eyes,dmg_mod:1,hit_mod:0,crit_mod:0,crit_dmg_mod:0,spec_flags:,auto_hit:0,dmg_scale:0,counter:0,magic_atk:0,ignore_onhit:0,dtype_rep:,retal_ok:1,auto_crit:0,fatal:1,ignore_closes:0,dmg_scale_post:,attack_num:1)
* atk_multi was 100. atk_bonus was 0. dmg_scale was 0.
* crit_multi was 126. crit_dmg_flat was 0. attack_num was 1.

After

Code:

System: Debug: Total Power for Staff of Eyes / Staff of Eyes was 56.
System: Debug: Before Use Skill called. Prinny, Senna, Sub-Attack, 1
System: Debug: Attack type: /obj/skill/fe_attack/sub. attack_nums:
System: Debug: Total Power for Staff of Eyes / Staff of Eyes was 56.
Senna attacks Prinny with Staff of Eyes!
Prinny takes 57 Light physical damage.
System:
* Initial Damage: 57 Light Physical, flags: , sk: null, wep: Staff of Eyes / /obj/items/equip/weapon/spears/staff_of_eyes
* play_atk_anim was 1.
* 0 Evade VS 246 Hit.  (Damage Hit Mod was 0)
*2 Roll(s) Remaining. This one was a hit.
*1 Roll(s) Remaining. This one was a hit.
* Critical check: 47 Critical VS 0 Critical Evade. (57)
* armor was allowed. armor_reduc was 0. (57)
* spec_flat_reduc was 0. (57)
* amp_multi was 1. (57)
* reduc_multi was 100. (57);  MAG DEF, 0 PHYS DEF, 100 REDUC
* elem_reduc was 0. (57)
* Damage caps applied. (57)
* Damage shields applied. (57)
* Final damage was: 57.
System: * basic_attack(atk:Senna,def:Prinny,W:Staff of Eyes,dmg_mod:1,hit_mod:0,crit_mod:0,crit_dmg_mod:0,spec_flags:,auto_hit:0,dmg_scale:0,counter:0,magic_atk:0,ignore_onhit:0,dtype_rep:,retal_ok:1,auto_crit:0,fatal:1,ignore_closes:0,dmg_scale_post:,attack_num:1)
* atk_multi was 100. atk_bonus was 0. dmg_scale was 0.
* crit_multi was 126. crit_dmg_flat was 0. attack_num was 1.
System: Debug: 0&&1
System: DEBUG: eye_restrict marker found at 77 with edge_limit of 1,1 to 42,46.

This applies to autohits as well.

[Senna]

Added onto this bug; it seems Analyze Weakness (Tested with the Staff of eye), if the target was inflicted with Dark eye, does not increase the level or duration.

[Neus]

This has been corrected. Dark Eye also only increases the values granted by the actual skill usage, not any application of the status.