Workflows are triggering twice after field updates are happening. Reevaluate workflows is turned off for all field updates. No specific updates on the record in after update triggers.
Log 1:
12:11:50.450 (2830002851)|CODE_UNIT_FINISHED|OpportunityTrigger on Opportunity trigger event AfterUpdate for [006c000000EPZrw]
12:11:50.450 (2831870864)|WF_FLOW_ACTION_BEGIN|09Lc00000004LRf
12:11:50.831 (2831959097)|FLOW_CREATE_INTERVIEW_BEGIN|00Dc0000003oW7m|30031000000Uc7F|301c00000009l5z
12:11:50.831 (2833786790)|FLOW_CREATE_INTERVIEW_END|618674d44f50b8609c9b57ec3e83153805fc75b-1d52|Opp- popeye Brand
12:11:50.834 (2834059074)|FLOW_START_INTERVIEWS_BEGIN|1
12:11:50.834 (2834535542)|FLOW_START_INTERVIEW_BEGIN|618674d44f50b8609c9b57ec3e83153805fc75b-1d52|Opp- popeye Brand
12:11:50.834 (2838451409)|FLOW_START_INTERVIEW_END|618674d44f50b8609c9b57ec3e83153805fc75b-1d52|Opp- popeye Brand
12:11:50.834 (2838463553)|FLOW_START_INTERVIEWS_END|1
12:11:50.450 (2840241557)|WF_FLOW_ACTION_END|09Lc00000004LRf
12:11:50.450 (2840314231)|WF_RULE_EVAL_BEGIN|Workflow
12:11:50.450 (2840345882)|WF_CRITERIA_BEGIN|[Opportunity: test2- 006c000000EPZrw]|Opportunity - Closed lost notification|01Qi0000000Dzqw|ON_CREATE_OR_TRIGGERING_UPDATE|1
12:11:50.450 (2840491415)|WF_FORMULA|Formula:ENCODED:[treatNullAsNull]{!ID:$User.Id} != {!ID:Owner} && ISPICKVAL({!ID:StageName},'Closed/Lost') && ( {!ID:$Profile.Name} != 'TW Operations' && {!ID:$Profile.Name} != 'TW System Administrator')|Values:OwnerId=005i0000002Wm4V, $Profile.Name=TW System Administrator, StageName=Closed/Won, $User.Id=005i0000004TZoh
12:11:50.450 (2840497613)|WF_CRITERIA_END|false
12:11:50.450 (2840515607)|WF_CRITERIA_BEGIN|[Opportunity: test2- 006c000000EPZrw]|Opportunity - Set Split % SE fields|01Qi0000000Pov3|ON_ALL_CHANGES|1
12:11:50.450 (2840611535)|WF_FORMULA|Formula:ENCODED:[treatNullAsNull]AND (OR( ISNEW() , ISCHANGED( {!ID:00Ni000000CCIln} ) , ISCHANGED( {!ID:00Ni000000CCIls} ) ) , {!ID:$User.00Ni000000D662p} = False)|Values:Sales_Engineer__c=005i0000002XRwK, $User.Bypass_Workflow_Rules__c=0, Sales_Engineer_2__c=005i0000002XRwK
12:11:50.450 (2840616329)|WF_CRITERIA_END|false
12:11:50.450 (2840632635)|WF_CRITERIA_BEGIN|[Opportunity: test2- 006c000000EPZrw]|Opportunity - Closed Order Notification-LAC|01Qi0000000Q04O|ON_CREATE_OR_TRIGGERING_UPDATE|1
And in second log, nothing happens after trigger execution ends. Issue is, if there is a process(process builder) active for an object, then after that process is executed(even if criteria in process matches or not), workflows(which doesnt met the criteria before) are triggered again. If no process active, then execution stops and commits the changes to the record