diff --git a/Sources/XcodeProj/XCProj/XCProjEncoder.swift b/Sources/XcodeProj/XCProj/XCProjEncoder.swift
index c9c41ecc9..d0c64abbb 100644
--- a/Sources/XcodeProj/XCProj/XCProjEncoder.swift
+++ b/Sources/XcodeProj/XCProj/XCProjEncoder.swift
@@ -33,8 +33,8 @@ final class XCProjEncoder {
     /// dictionary on every access.
     private var targetAttributes: [PBXTarget: [String: ProjectAttribute]] = [:]
 
-    /// Build phases that can only be referred to by identifier, because their target has more than
-    /// one phase of the same kind and name.
+    /// Build phases that can only be referred to by identifier, because a name based reference
+    /// would not pick them out.
     private var ambiguousPhases: Set<PBXObjectReference> = []
 
     /// The target that owns each build phase.
@@ -176,6 +176,20 @@ extension XCProjEncoder {
             for (phase, key) in keyed where counts[key, default: 0] > 1 {
                 ambiguousPhases.insert(phase.reference)
             }
+            for (phase, key) in keyed where key.name == nil && Self.isRepeatableKind(key.kind) {
+                ambiguousPhases.insert(phase.reference)
+            }
+        }
+    }
+
+    /// Whether a target can hold more than one build phase of this kind.
+    ///
+    /// Xcode resolves `"App/resources"` against the single phase of that kind, but rejects
+    /// `"App/copy"` and `"App/script"` even when the target holds one, so those need an identifier.
+    private static func isRepeatableKind(_ kind: BuildPhase) -> Bool {
+        switch kind {
+        case .copyFiles, .runScript: true
+        case .sources, .frameworks, .resources, .headers, .carbonResources: false
         }
     }
 
diff --git a/Tests/XcodeProjTests/XCProj/XCProjEncoderTests.swift b/Tests/XcodeProjTests/XCProj/XCProjEncoderTests.swift
index eca044925..a96f237d4 100644
--- a/Tests/XcodeProjTests/XCProj/XCProjEncoderTests.swift
+++ b/Tests/XcodeProjTests/XCProj/XCProjEncoderTests.swift
@@ -173,6 +173,56 @@ import XcodeProjectFormat
         )
     }
 
+    /// Xcode rejects `"App/copy"` and `"App/script"` with "Could not uniquely resolve the build
+    /// phase name" even when the target holds one, because it can hold many. Apple's schema
+    /// validator accepts both spellings, so only an identifier makes such a phase addressable.
+    @Test(arguments: ["CopyFiles", "Run Script", "Sources", "Frameworks", "Resources", "Headers"])
+    func namelessRepeatablePhasesCarryAnIdentifier(rawKind: String) throws {
+        let kind = try #require(BuildPhase(rawValue: rawKind))
+        let phase: PBXBuildPhase = switch kind {
+        case .copyFiles: PBXCopyFilesBuildPhase(dstPath: "include", dstSubfolderSpec: .productsDirectory)
+        case .runScript: PBXShellScriptBuildPhase(shellScript: "echo hi")
+        case .sources: PBXSourcesBuildPhase()
+        case .frameworks: PBXFrameworksBuildPhase()
+        case .resources: PBXResourcesBuildPhase()
+        default: PBXHeadersBuildPhase()
+        }
+        let file = PBXFileReference(sourceTree: .group, path: "Main.swift")
+        let buildFile = PBXBuildFile(file: file)
+        phase.files = [buildFile]
+
+        let configuration = XCBuildConfiguration(name: "Release")
+        let targetList = XCConfigurationList(buildConfigurations: [configuration], defaultConfigurationName: "Release")
+        let target = PBXNativeTarget(name: "App", buildConfigurationList: targetList, buildPhases: [phase])
+        let mainGroup = PBXGroup(children: [file], sourceTree: .group)
+        let proj = try Self.makeProj(
+            mainGroup: mainGroup,
+            target: target,
+            extraObjects: [phase, file, buildFile, configuration]
+        )
+
+        let schemaKind = switch kind {
+        case .copyFiles: "copy"
+        case .runScript: "script"
+        case .sources: "compile-sources"
+        default: rawKind.lowercased()
+        }
+        let data = try proj.xcprojData()
+        let emittedByName = String(decoding: data, as: UTF8.self).contains("\"App/\(schemaKind)\"")
+        let repeatable = kind == .copyFiles || kind == .runScript
+
+        #expect(
+            emittedByName == !repeatable,
+            repeatable
+                ? "a nameless \(schemaKind) phase is not addressable by name and needs an identifier"
+                : "a target holds one \(schemaKind) phase, so the name is enough"
+        )
+
+        // Whichever spelling it is, the membership has to survive the trip back.
+        let decoded = try PBXProj(xcprojData: data, projectName: "App")
+        #expect(decoded.rootObject?.targets.first?.buildPhases.first?.files?.count == 1)
+    }
+
     // MARK: - Ambiguity
 
     @Test func usesIdentifiersForAmbiguousNames() throws {