Linden tells Holder she used her service weapon to kill the cow. When she shot the cow she had left Seattle PD and was working on the ferry, and didn't have a service weapon. She used her personal Sig Sauer pistol, not the department-issued Glocks used throughout the series.
Holder suggests to Linden that Kyle may not have planned to kill himself but instead made the decision to do so after sitting with the bodies for hours. The neighbor called 911 after hearing the gunshots so it could not have been hours before police arrived. Holder should have known this.
When Holder comes to Linden's home in the morning. Neither door is locked. It's highly unlikely she'd leave her doors unlocked.