I activate Bellows Breathe to target 3 units in base and repeat it to target 1 unit at Battlefield A. Can my opponent use Repulse to counter the Bellows Breathe, or will it only counter 1 of the repeats?

Your opponent cannot use Repulse to counter your repeated Bellows Breath.

Reasoning

According to the established RiftJudge FAQ #9655 and #10127:

1. Repulse's Targeting Constraint: Repulse can only be used as a reaction to an enemy spell or ability if it targets exactly one friendly unit and no other friendly unit.
2. Bellows Breath's Total Targeting Scope: When you pay the Repeat cost for Bellows Breath, the spell is played once, but its effect is executed twice upon resolution. Per Rule 820.3.a, the spell is only played once, but its targeting scope for the purpose of the chain includes every unit targeted across both executions.
3. Interaction: In your scenario, you chose three units at your base (the first execution) and one unit at a battlefield (the second execution). Because your repeated Bellows Breath is targeting a total of four units across its two executions, it fails the requirement of Repulse, which requires the spell to target exactly one friendly unit and "no other friendly units."

Summary of Timing

• Bellows Breath is played as an [Action].
• When you pay the Repeat cost, you are finalizing the spell on the chain with all four targets (three in base, one at battlefield A) chosen at once.
• Because the spell's total target count is four, it does not meet the "exactly one" requirement for Repulse. Consequently, Repulse is not a legal reaction to this spell instance.